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# Data listing for medium sized (<50Mb) data files
# Annotation
data/hpc/annotation/all_ipr.tsv
data/hpc/annotation/Adigitifera_uniprot_blastp.outfmt6
data/hpc/annotation/Adigitifera_uniprot_blastx.outfmt6
data/hpc/annotation/uniprot-yourlist.tab
data/hpc/annotation/uniprot_gene_annot.tsv
data/hpc/annotation/allgenes_ids_extracted_from_gff.txt
data/hpc/annotation/uniprot_gene_annot.tsv
# Simulated data under FSC model
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC.est
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC.tpl
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/admixture/3.out.growth_rate_SC_1_1.fam
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/admixture/3.out.growth_rate_SC_ldpruned.3.Q
cache/hbd_data.rds
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/10_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/1_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/2_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/3_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/4_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/5_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/6_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/7_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/8_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/plink2/9_1.het
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_10_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_10_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_10_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_1_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_1_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_1_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_2_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_2_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_2_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_3_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_3_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_3_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_4_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_4_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_4_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_5_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_5_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_5_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_6_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_6_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_6_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_7_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_7_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_7_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_8_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_8_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_8_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_9_1.gen.vcf.gz_IN_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_9_1.gen.vcf.gz_NO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/tajima/3.out.growth_rate_SC_9_1.gen.vcf.gz_SO_1based.td
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/10_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/11_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/12_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/13_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/14_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/15_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/16_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/17_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/18_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/19_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/1_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/20_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/21_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/22_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/23_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/24_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/25_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/26_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/27_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/28_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/29_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/2_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/30_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/31_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/32_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/33_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/34_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/35_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/36_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/37_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/38_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/39_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/3_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/40_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/41_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/42_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/43_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/44_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/45_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/46_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/47_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/48_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/49_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/4_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/50_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/5_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/6_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/7_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/8_1.pbs
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/pbs/9_1.pbs
# Kraken profiling
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_1_001_S102_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_1_008_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_1_021_S97_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_1_022_S98_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_1_023_S101_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_1_025_S99_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_2_036_S105_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_2_041_S107_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_2_043_S106_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_2_136_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_2_151_S103_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_3_047_S110_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_3_060_S109_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_3_063_S108_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AI_3_071_S111_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_125_374_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_125_377_S131_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_125_385_S127_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_125_388_S128_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_125_392_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_128_316_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_128_318_S135_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_128_326_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_128_328_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_128_336_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_132_154_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_132_162_S140_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_132_170_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_132_173_S141_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_132_178_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_133_341_S143_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_133_343_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_133_346_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_133_354_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/AR_133_357_S142_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_4_077_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_4_078_S116_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_4_081_S118_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_4_082_S117_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_4_087_S112_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_4_088_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_4_091_S113_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_4_100_S119_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_5_112_S122_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_5_114_S126_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_5_121_S125_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_5_123_S121_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_5_124_S124_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_5_129_S120_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/BR_5_133_S123_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099286.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099287.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099291.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099303.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099319.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099320.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099350.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099351.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099361.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099370.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099377.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099383.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099391.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099398.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099421.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/DRR099428.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS1_2_417_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS1_2_422_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS1_M11_820_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS1_M11_840_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS1_M12_808_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS1_M12_817_S151_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS1_S_314_S154_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS1_S_321_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_2_256_S155_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_C11_769_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_C11_784_S156_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_C13_704_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_C13_706_S159_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_C13_721_S158_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_C20_283_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_S_734_S162_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS2_S_737_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS3_1_184_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS3_1_185_S166_L004.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS3_1_191_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS3_1_207_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS3_S_215_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS3_S_232_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS3_S_246_merged.mpa
data/hpc/symbiodinium_profiles/genome_kraken_mpa/RS3_S_250_merged.mpa
# Radseq Checks
data/hpc/radseq_data/out.relatedness2
data/hpc/radseq_data/Sample_list_Jia_popgen_141121.xlsx
data/hpc/radseq_data/Complete_list_Adigi_Ashmore_Adele_Beagle_Rowleys_181121.xlsx
# IGV Tracks and track creation
data/hpc/tracks/01_gather_data.sh
data/hpc/tracks/02_tajima_to_wig.sh
data/hpc/tracks/03_pi_to_wig.sh
data/hpc/tracks/04_pbs_to_wig.sh
data/hpc/tracks/05_bamcov.sh
data/hpc/tracks/GCA_014634065.1_Adig_2.0_genomic.fna
data/hpc/tracks/GCA_014634065.1_Adig_2.0_genomic.fna.fai
data/hpc/tracks/adig-v2.gff
data/hpc/tracks/adig2_chromsizes.txt
data/hpc/tracks/fst.slidingwindow.tsv
data/hpc/tracks/fst2wig.awk
data/hpc/tracks/inshore.pestPG
data/hpc/tracks/inshore_TajimaD.bw
data/hpc/tracks/inshore_TajimaD.wig
data/hpc/tracks/inshore_ThetaD.bw
data/hpc/tracks/inshore_ThetaD.wig
data/hpc/tracks/inshore_pbs.bw
data/hpc/tracks/inshore_pbs.wig
data/hpc/tracks/inshore_readcov.bw
data/hpc/tracks/north_offshore.pestPG
data/hpc/tracks/north_offshore_TajimaD.bw
data/hpc/tracks/north_offshore_TajimaD.wig
data/hpc/tracks/north_offshore_ThetaD.bw
data/hpc/tracks/north_offshore_ThetaD.wig
data/hpc/tracks/north_offshore_pbs.bw
data/hpc/tracks/north_offshore_pbs.wig
data/hpc/tracks/north_offshore_readcov.bw
data/hpc/tracks/south_offshore.pestPG
data/hpc/tracks/south_offshore_TajimaD.bw
data/hpc/tracks/south_offshore_TajimaD.wig
data/hpc/tracks/south_offshore_ThetaD.bw
data/hpc/tracks/south_offshore_ThetaD.wig
data/hpc/tracks/south_offshore_pbs.bw
data/hpc/tracks/south_offshore_pbs.wig
data/hpc/tracks/south_offshore_readcov.bw
data/hpc/tracks/sweeps.gff3
data/hpc/tracks/theta2wig.awk
# IQTree
data/hpc/iqtree/partition.nex.best_scheme.nex.treefile
# PCAngsd Files
data/hpc/pcangsd/samples.txt
data/hpc/pcangsd/all_bam.txt
data/hpc/pcangsd/jpwa.cov
data/hpc/pcangsd/jpwa.tree
data/hpc/pcangsd/wa.sites
data/hpc/pcangsd/wa.cov
data/hpc/pcangsd/wa_bam.txt
# RagTag
data/hpc/ragtag/ragtag_output/ragtag.scaffolds.agp
data/hpc/ragtag/all.lengths.scaf.txt
# Thetastat
data/hpc/thetastat/inshore.pestPG
data/hpc/thetastat/north_offshore.pestPG
data/hpc/thetastat/south_offshore.pestPG
data/hpc/thetastat/fst.slidingwindow.tsvAI_1_001_S102_L004_bamtools.stats
data/hpc/thetastat/fst.slidingwindow.tsv
# Bamstats
data/hpc/bamstats/AR_125_385_S127_L004_bamtools.stats
data/hpc/bamstats/RS3_S_215_merged_bamtools.stats
data/hpc/bamstats/RS3_1_191_merged_bamtools.stats
data/hpc/bamstats/BR_4_081_S118_L004_bamtools.stats
data/hpc/bamstats/RS3_1_185_S166_L004_bamtools.stats
data/hpc/bamstats/AR_133_346_merged_bamtools.stats
data/hpc/bamstats/AR_125_388_S128_L004_bamtools.stats
data/hpc/bamstats/BR_4_100_S119_L004_bamtools.stats
data/hpc/bamstats/RS1_M12_817_S151_L004_bamtools.stats
data/hpc/bamstats/RS2_C11_784_S156_L004_bamtools.stats
data/hpc/bamstats/RS3_1_207_merged_bamtools.stats
data/hpc/bamstats/BR_5_124_S124_L004_bamtools.stats
data/hpc/bamstats/BR_4_078_S116_L004_bamtools.stats
data/hpc/bamstats/AI_2_043_S106_L004_bamtools.stats
data/hpc/bamstats/AR_132_173_S141_L004_bamtools.stats
data/hpc/bamstats/RS1_2_422_merged_bamtools.stats
data/hpc/bamstats/AR_133_354_merged_bamtools.stats
data/hpc/bamstats/RS2_C20_283_merged_bamtools.stats
data/hpc/bamstats/AI_3_060_S109_L004_bamtools.stats
data/hpc/bamstats/RS2_C13_706_S159_L004_bamtools.stats
data/hpc/bamstats/AR_133_357_S142_L004_bamtools.stats
data/hpc/bamstats/BR_5_133_S123_L004_bamtools.stats
data/hpc/bamstats/BR_5_121_S125_L004_bamtools.stats
data/hpc/bamstats/RS1_S_314_S154_L004_bamtools.stats
data/hpc/bamstats/RS1_M12_808_merged_bamtools.stats
data/hpc/bamstats/AI_2_151_S103_L004_bamtools.stats
data/hpc/bamstats/RS2_C13_704_merged_bamtools.stats
data/hpc/bamstats/BR_5_129_S120_L004_bamtools.stats
data/hpc/bamstats/BR_5_112_S122_L004_bamtools.stats
data/hpc/bamstats/BR_4_088_merged_bamtools.stats
data/hpc/bamstats/AR_133_341_S143_L004_bamtools.stats
data/hpc/bamstats/AR_132_170_merged_bamtools.stats
data/hpc/bamstats/RS1_S_321_merged_bamtools.stats
data/hpc/bamstats/AR_132_154_merged_bamtools.stats
data/hpc/bamstats/AR_132_178_merged_bamtools.stats
data/hpc/bamstats/AI_2_036_S105_L004_bamtools.stats
data/hpc/bamstats/AI_1_001_S102_L004_bamtools.stats
data/hpc/bamstats/AR_125_377_S131_L004_bamtools.stats
data/hpc/bamstats/BR_4_087_S112_L004_bamtools.stats
data/hpc/bamstats/BR_5_114_S126_L004_bamtools.stats
data/hpc/bamstats/AR_128_316_merged_bamtools.stats
data/hpc/bamstats/RS2_C11_769_merged_bamtools.stats
data/hpc/bamstats/RS2_S_734_S162_L004_bamtools.stats
data/hpc/bamstats/BR_5_123_S121_L004_bamtools.stats
data/hpc/bamstats/AR_132_162_S140_L004_bamtools.stats
data/hpc/bamstats/AI_1_025_S99_L004_bamtools.stats
data/hpc/bamstats/AR_125_374_merged_bamtools.stats
data/hpc/bamstats/BR_4_091_S113_L004_bamtools.stats
data/hpc/bamstats/RS3_S_232_merged_bamtools.stats
data/hpc/bamstats/AR_128_326_merged_bamtools.stats
data/hpc/bamstats/RS2_S_737_merged_bamtools.stats
data/hpc/bamstats/RS1_2_417_merged_bamtools.stats
data/hpc/bamstats/RS3_1_184_merged_bamtools.stats
data/hpc/bamstats/AI_3_047_S110_L004_bamtools.stats
data/hpc/bamstats/AI_1_008_merged_bamtools.stats
data/hpc/bamstats/RS2_C13_721_S158_L004_bamtools.stats
data/hpc/bamstats/RS1_M11_820_merged_bamtools.stats
data/hpc/bamstats/AR_128_328_merged_bamtools.stats
data/hpc/bamstats/BR_4_082_S117_L004_bamtools.stats
data/hpc/bamstats/BR_4_077_merged_bamtools.stats
data/hpc/bamstats/AR_133_343_merged_bamtools.stats
data/hpc/bamstats/RS1_M11_840_merged_bamtools.stats
data/hpc/bamstats/AI_3_071_S111_L004_bamtools.stats
data/hpc/bamstats/AR_128_336_merged_bamtools.stats
data/hpc/bamstats/AI_2_136_merged_bamtools.stats
data/hpc/bamstats/AI_1_021_S97_L004_bamtools.stats
data/hpc/bamstats/RS2_2_256_S155_L004_bamtools.stats
data/hpc/bamstats/RS3_S_250_merged_bamtools.stats
data/hpc/bamstats/AI_2_041_S107_L004_bamtools.stats
data/hpc/bamstats/RS3_S_246_merged_bamtools.stats
data/hpc/bamstats/AR_125_392_merged_bamtools.stats
data/hpc/bamstats/AI_3_063_S108_L004_bamtools.stats
data/hpc/bamstats/AR_128_318_S135_L004_bamtools.stats
data/hpc/bamstats/AI_1_022_S98_L004_bamtools.stats
data/hpc/bamstats/AI_1_023_S101_L004_bamtools.stats
# Admixture
data/hpc/admixture/Adigitifera_ldpruned.6.Q
data/hpc/admixture/Adigitifera_ldpruned.2.Q
data/hpc/admixture/Adigitifera_ldpruned.5.Q
data/hpc/admixture/Adigitifera_ldpruned.1.Q
data/hpc/admixture/sample_order.txt
data/hpc/admixture/Adigitifera_ldpruned.4.Q
data/hpc/admixture/CV.txt
data/hpc/admixture/Adigitifera_ldpruned.3.Q
# Demography
data/hpc/demography/estimate_em50_k40
data/hpc/demography/estimate_em50_k40/inshore.final.json
data/hpc/demography/estimate_em50_k40/em50_k40.png
data/hpc/demography/estimate_em50_k40/em50_k40.csv
data/hpc/demography/estimate_em50_k40/northoffshore.final.json
data/hpc/demography/estimate_em50_k40/southoffshore.final.json
# genomeCov
data/hpc/genomeCov/BR_5_129_S120_L004_coverage.txt
data/hpc/genomeCov/AR_125_392_merged_coverage.txt
data/hpc/genomeCov/AR_133_346_merged_coverage.txt
data/hpc/genomeCov/BR_5_114_S126_L004_coverage.txt
data/hpc/genomeCov/AI_1_022_S98_L004_coverage.txt
data/hpc/genomeCov/AI_2_036_S105_L004_coverage.txt
data/hpc/genomeCov/AR_133_357_S142_L004_coverage.txt
data/hpc/genomeCov/AR_132_178_merged_coverage.txt
data/hpc/genomeCov/AI_2_041_S107_L004_coverage.txt
data/hpc/genomeCov/AR_125_377_S131_L004_coverage.txt
data/hpc/genomeCov/BR_5_124_S124_L004_coverage.txt
data/hpc/genomeCov/RS2_C13_704_merged_coverage.txt
data/hpc/genomeCov/BR_5_123_S121_L004_coverage.txt
data/hpc/genomeCov/AR_132_173_S141_L004_coverage.txt
data/hpc/genomeCov/RS1_M12_808_merged_coverage.txt
data/hpc/genomeCov/AI_1_021_S97_L004_coverage.txt
data/hpc/genomeCov/RS2_S_737_merged_coverage.txt
data/hpc/genomeCov/BR_4_081_S118_L004_coverage.txt
data/hpc/genomeCov/AI_1_008_merged_coverage.txt
data/hpc/genomeCov/AR_133_343_merged_coverage.txt
data/hpc/genomeCov/RS3_S_232_merged_coverage.txt
data/hpc/genomeCov/BR_4_091_S113_L004_coverage.txt
data/hpc/genomeCov/RS1_2_422_merged_coverage.txt
data/hpc/genomeCov/RS2_C11_784_S156_L004_coverage.txt
data/hpc/genomeCov/AR_132_170_merged_coverage.txt
data/hpc/genomeCov/BR_5_112_S122_L004_coverage.txt
data/hpc/genomeCov/AI_2_136_merged_coverage.txt
data/hpc/genomeCov/AR_128_316_merged_coverage.txt
data/hpc/genomeCov/AR_133_354_merged_coverage.txt
data/hpc/genomeCov/BR_4_100_S119_L004_coverage.txt
data/hpc/genomeCov/RS1_M11_840_merged_coverage.txt
data/hpc/genomeCov/BR_5_121_S125_L004_coverage.txt
data/hpc/genomeCov/RS1_S_314_S154_L004_coverage.txt
data/hpc/genomeCov/RS2_C11_769_merged_coverage.txt
data/hpc/genomeCov/RS1_M12_817_S151_L004_coverage.txt
data/hpc/genomeCov/AI_3_060_S109_L004_coverage.txt
data/hpc/genomeCov/AI_1_023_S101_L004_coverage.txt
data/hpc/genomeCov/AR_125_388_S128_L004_coverage.txt
data/hpc/genomeCov/RS2_C13_706_S159_L004_coverage.txt
data/hpc/genomeCov/AR_125_374_merged_coverage.txt
data/hpc/genomeCov/AI_2_043_S106_L004_coverage.txt
data/hpc/genomeCov/AI_3_063_S108_L004_coverage.txt
data/hpc/genomeCov/BR_4_082_S117_L004_coverage.txt
data/hpc/genomeCov/AI_1_001_S102_L004_coverage.txt
data/hpc/genomeCov/RS2_C13_721_S158_L004_coverage.txt
data/hpc/genomeCov/RS3_1_191_merged_coverage.txt
data/hpc/genomeCov/AI_3_071_S111_L004_coverage.txt
data/hpc/genomeCov/BR_4_088_merged_coverage.txt
data/hpc/genomeCov/RS3_S_215_merged_coverage.txt
data/hpc/genomeCov/AR_128_326_merged_coverage.txt
data/hpc/genomeCov/RS2_C20_283_merged_coverage.txt
data/hpc/genomeCov/RS1_S_321_merged_coverage.txt
data/hpc/genomeCov/BR_4_078_S116_L004_coverage.txt
data/hpc/genomeCov/RS1_M11_820_merged_coverage.txt
data/hpc/genomeCov/AI_3_047_S110_L004_coverage.txt
data/hpc/genomeCov/RS3_1_185_S166_L004_coverage.txt
data/hpc/genomeCov/RS3_S_246_merged_coverage.txt
data/hpc/genomeCov/AR_132_154_merged_coverage.txt
data/hpc/genomeCov/AR_128_328_merged_coverage.txt
data/hpc/genomeCov/AR_132_162_S140_L004_coverage.txt
data/hpc/genomeCov/BR_4_087_S112_L004_coverage.txt
data/hpc/genomeCov/AR_128_318_S135_L004_coverage.txt
data/hpc/genomeCov/BR_4_077_merged_coverage.txt
data/hpc/genomeCov/RS3_S_250_merged_coverage.txt
data/hpc/genomeCov/AI_1_025_S99_L004_coverage.txt
data/hpc/genomeCov/BR_5_133_S123_L004_coverage.txt
data/hpc/genomeCov/RS2_S_734_S162_L004_coverage.txt
data/hpc/genomeCov/RS3_1_184_merged_coverage.txt
data/hpc/genomeCov/RS1_2_417_merged_coverage.txt
data/hpc/genomeCov/RS2_2_256_S155_L004_coverage.txt
data/hpc/genomeCov/AR_133_341_S143_L004_coverage.txt
data/hpc/genomeCov/RS3_1_207_merged_coverage.txt
data/hpc/genomeCov/AI_2_151_S103_L004_coverage.txt
data/hpc/genomeCov/AR_128_336_merged_coverage.txt
data/hpc/genomeCov/AR_125_385_S127_L004_coverage.txt
# ibd
data/hpc/ibd/Adigi.ibd.ne.ne
data/hpc/ibd/Adigi_ind74.ibd_relatedness.txt
data/hpc/ibdseq/1M_scaffolds.hbd
data/hpc/ibdseq/hbd_midpoints.txt
data/hpc/pcangsd/all.lengths.scaf.txt
data/hpc/ibdseq/hbd_midpoints.scaff.txt
# pca
data/hpc/pca/Adigitifera_smartpca.fst
data/hpc/pca/Adigitifera_smartpca.eval
data/hpc/pca/Adigitifera_smartpca.evec
data/hpc/pca/Adigitifera_smartpca.snpeigs
# phasing
data/hpc/phasing/imputation_check.txt
data/hpc/phasing/compare_imputation_with_af.txt
# popgen
data/hpc/popgen/plink2.het
data/hpc/popgen/southoffshore.filtered_windowed.td
data/hpc/popgen/inshore_northoffshore_per_snp_fst.weir.fst
data/hpc/popgen/southoffshore.ld
data/hpc/popgen/inshore.ld
data/hpc/popgen/inshore.filtered_windowed.td
data/hpc/popgen/northoffshore.filtered_windowed.pi
data/hpc/popgen/northoffshore.filtered_windowed.td
data/hpc/popgen/northoffshore_southoffshore_per_snp_fst.weir.fst
data/hpc/popgen/inshore_southoffshore_per_snp_fst.weir.fst
data/hpc/popgen/inshore.filtered_windowed.pi
data/hpc/popgen/southoffshore.filtered_windowed.pi
# vcf_filtering
data/hpc/vcf_filtering/Adigi.v2.filtered.snpden
data/hpc/vcf_filtering/Adigi.v2.filtered.idepth
data/hpc/vcf_filtering/Adigi.v2.filtered.imiss
# selection
data/hpc/selection2/pbs/max_pbs_in_sweeps.tsv
data/hpc/selection2/pbs/pbs_nosweeps.tsv
data/hpc/selection2/pbs/pbs_sweeps.scaff.tsv
data/hpc/selection2/pbs/pbs_sweeps.tsv
data/hpc/selection2/pbs/plink2.IN.NO.fst.var
data/hpc/selection2/pbs/plink2.IN.SO.fst.var
data/hpc/selection2/pbs/plink2.NO.SO.fst.var
data/hpc/selection2/pbs/plink2.fst.summary
data/hpc/selection2/pbs/plink2.log
data/hpc/selection2/pbs/plink2.pbs
data/hpc/selection2/pbs/plink2.pbs_scaff.tsv
data/hpc/selection2/pbs/plink2_noheader.bed
data/hpc/selection2/pbs/plink2_noheader.pbs
data/hpc/selection2/pbs/plink2_noheader_sorted.bed
data/hpc/selection2/xpnsl/southoffshore_vs_inshore_northoffshore.xpnsl.norm.50kb.windows
data/hpc/selection2/xpnsl/northoffshore_vs_inshore_southoffshore.xpnsl.norm
data/hpc/selection2/xpnsl/inshore_vs_offshore.xpnsl.norm.50kb.windows
data/hpc/selection2/xpnsl/northoffshore_vs_inshore_southoffshore.xpnsl.norm.50kb.windows
data/hpc/selection2/xpnsl/inshore_vs_offshore.xpnsl.norm
data/hpc/selection2/xpnsl/southoffshore_vs_inshore_northoffshore.xpnsl.norm
data/hpc/selection2/xpnsl/northoffshore_vs_inshore_southoffshore.xpnsl.norm.ragtag.txt
data/hpc/selection2/xpnsl/southoffshore_vs_inshore_northoffshore.xpnsl.norm.ragtag.txt
data/hpc/selection2/xpnsl/inshore_vs_offshore.xpnsl.norm.ragtag.txt
data/hpc/selection2/ihs/inshore.ihs.50bins.norm.50kb.windows
data/hpc/selection2/ihs/northoffshore.ihs.50bins.norm
data/hpc/selection2/ihs/southoffshore.ihs.50bins.norm
data/hpc/selection2/ihs/southoffshore.ihs.50bins.norm.ragtag.txt
data/hpc/selection2/ihs/southoffshore.ihs.50bins.norm.50kb.windows
data/hpc/selection2/ihs/inshore.ihs.50bins.norm
data/hpc/selection2/ihs/northoffshore.ihs.50bins.norm.ragtag.txt
data/hpc/selection2/ihs/northoffshore.ihs.50bins.norm.50kb.windows
data/hpc/selection2/ihs/inshore.ihs.50bins.norm.ragtag.txt
data/hpc/selection2/xpehh/inshore_vs_offshore.xpehh.norm
data/hpc/selection2/xpehh/northoffshore_vs_inshore_southoffshore.xpehh.norm
data/hpc/selection2/xpehh/southoffshore_vs_inshore_northoffshore.xpehh.norm.50kb.windows
data/hpc/selection2/xpehh/northoffshore_vs_inshore_southoffshore.xpehh.norm.ragtag.txt
data/hpc/selection2/xpehh/inshore_vs_offshore.xpehh.norm.50kb.windows
data/hpc/selection2/xpehh/northoffshore_vs_inshore_southoffshore.xpehh.norm.50kb.windows
data/hpc/selection2/xpehh/southoffshore_vs_inshore_northoffshore.xpehh.norm.ragtag.txt
data/hpc/selection2/xpehh/inshore_vs_offshore.xpehh.norm.ragtag.txt
data/hpc/selection2/xpehh/southoffshore_vs_inshore_northoffshore.xpehh.norm
# finestructure
data/hpc/fineStructure/FinestructureRcode/FinestructureLibrary.R
data/hpc/fineStructure/adigitifera_linked.chunkcounts.out
data/hpc/fineStructure/adigitifera_linked_mcmc.xml
data/hpc/fineStructure/adigitifera_linked_tree.xml
# annotation
data/hpc/annotation/Adigitifera_uniprot_blastp.outfmt6
data/hpc/annotation/Adigitifera_uniprot_blastx.outfmt6
data/hpc/annotation/adig_iprscan_withgo.tsv
data/hpc/annotation/allgenes.bed
data/hpc/annotation/allgenes_ids_extracted_from_gff.txt
data/hpc/annotation/annotation_from_chuya
data/hpc/annotation/gene-to-go_topgo.tsv
data/hpc/annotation/uniprot-yourlist.tab
data/hpc/annotation/uniprot_gene_annot.tsv
data/hpc/annotation/uniprot_id_gene_name.tab
# startmrca
data/hpc/startmrca/02_furcation_plots.sh
data/hpc/startmrca/03_run_tmrca.sh
data/hpc/startmrca/04_runqc_plots.sh
data/hpc/startmrca/05_haplostrips.sh
data/hpc/startmrca/qsub_template.sh
data/hpc/startmrca/run_furcation.R
data/hpc/startmrca/run_qc.R
data/hpc/startmrca/run_startmrca.R
data/hpc/startmrca/sweep_regions.xlsx
data/hpc/startmrca/sweep_regions.tsv
data/hpc/startmrca/sweep_regions_checked.tsv
data/hpc/startmrca/qc_plots/BLFC01000007_450000_500001.pdf
data/hpc/startmrca/qc_plots/BLFC01000008_1150000_1200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000008_2050000_2100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000016_1050000_1100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000016_3200000_3250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000039_100000_150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000047_1150000_1300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000047_750000_800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000047_950000_1000001.pdf
data/hpc/startmrca/qc_plots/BLFC01000051_2800000_2850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000051_3050000_3100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000051_3400000_3500001.pdf
data/hpc/startmrca/qc_plots/BLFC01000051_3550000_3600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000051_400000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000051_600000_650001.pdf
data/hpc/startmrca/qc_plots/BLFC01000055_150000_250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000056_1050000_1100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000056_950000_1000001.pdf
data/hpc/startmrca/qc_plots/BLFC01000057_650000_700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000074_100000_250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000074_1200000_1250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000082_550000_600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000089_100000_200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000100_1550000_1700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000100_2200000_2250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000100_3250000_3350001.pdf
data/hpc/startmrca/qc_plots/BLFC01000100_800000_850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000123_1650000_1750001.pdf
data/hpc/startmrca/qc_plots/BLFC01000123_850000_900001.pdf
data/hpc/startmrca/qc_plots/BLFC01000124_650000_700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000125_1600000_1650001.pdf
data/hpc/startmrca/qc_plots/BLFC01000137_350000_400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000137_650000_850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000148_600000_800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000152_2400000_2450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000152_50000_100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000154_0_50001.pdf
data/hpc/startmrca/qc_plots/BLFC01000154_250000_300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000158_700000_750001.pdf
data/hpc/startmrca/qc_plots/BLFC01000161_700000_750001.pdf
data/hpc/startmrca/qc_plots/BLFC01000166_1100000_1150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000174_50000_100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000184_1600000_1650001.pdf
data/hpc/startmrca/qc_plots/BLFC01000185_100000_300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000185_1550000_1600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000185_900000_1050001.pdf
data/hpc/startmrca/qc_plots/BLFC01000201_1300000_1350001.pdf
data/hpc/startmrca/qc_plots/BLFC01000201_150000_200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000201_2350000_2400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000201_800000_850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000208_350000_400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000211_650000_700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000235_3050000_3100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000243_650000_700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000255_450000_500001.pdf
data/hpc/startmrca/qc_plots/BLFC01000255_450000_600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000255_50000_300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000256_1300000_1400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000256_400000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000265_200000_250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000274_600000_650001.pdf
data/hpc/startmrca/qc_plots/BLFC01000277_150000_250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000286_1950000_2000001.pdf
data/hpc/startmrca/qc_plots/BLFC01000289_450000_500001.pdf
data/hpc/startmrca/qc_plots/BLFC01000298_1250000_1300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000298_1300000_1350001.pdf
data/hpc/startmrca/qc_plots/BLFC01000298_200000_350001.pdf
data/hpc/startmrca/qc_plots/BLFC01000298_550000_600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000309_2150000_2200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000309_2200000_2300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000309_2950000_3100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000309_400000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000310_200000_250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000310_2100000_2150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000317_1000000_1050001.pdf
data/hpc/startmrca/qc_plots/BLFC01000324_1200000_1400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000324_1600000_1800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000324_350000_400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000326_1550000_2150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000341_1500000_1550001.pdf
data/hpc/startmrca/qc_plots/BLFC01000341_1750000_1800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000341_950000_1000001.pdf
data/hpc/startmrca/qc_plots/BLFC01000348_1350000_1400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000348_2050000_2150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000348_2400000_2450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000375_100000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000393_1400000_1450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000393_1650000_1700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000404_1000000_1050001.pdf
data/hpc/startmrca/qc_plots/BLFC01000404_1250000_1300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000407_1800000_2050001.pdf
data/hpc/startmrca/qc_plots/BLFC01000410_1050000_1100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000413_150000_200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000427_850000_900001.pdf
data/hpc/startmrca/qc_plots/BLFC01000439_1750000_1800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000439_2650000_2700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000450_1550000_1600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000450_750000_800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000451_750000_800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000454_300000_400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000454_400000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000468_300000_400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000480_800000_900001.pdf
data/hpc/startmrca/qc_plots/BLFC01000511_800000_850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000522_1650000_1750001.pdf
data/hpc/startmrca/qc_plots/BLFC01000536_200000_250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000542_200000_300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000557_300000_350001.pdf
data/hpc/startmrca/qc_plots/BLFC01000557_550000_600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000565_100000_150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000573_150000_200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000583_50000_100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000591_150000_200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000593_400000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000596_1400000_1450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000596_3450000_3500001.pdf
data/hpc/startmrca/qc_plots/BLFC01000596_550000_600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000599_750000_800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000600_2250000_2300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000600_2900000_2950001.pdf
data/hpc/startmrca/qc_plots/BLFC01000600_3650000_3700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000600_3700000_3800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000600_400000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000610_900000_1100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000632_1650000_1700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000632_2550000_3150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000632_2950000_3000001.pdf
data/hpc/startmrca/qc_plots/BLFC01000632_550000_600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000639_1300000_1550001.pdf
data/hpc/startmrca/qc_plots/BLFC01000639_2100000_2150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000645_400000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000647_1450000_1500001.pdf
data/hpc/startmrca/qc_plots/BLFC01000647_200000_250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000647_2800000_2850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000647_3000000_3050001.pdf
data/hpc/startmrca/qc_plots/BLFC01000653_2050000_2150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000655_200000_250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000660_700000_750001.pdf
data/hpc/startmrca/qc_plots/BLFC01000690_2600000_2850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000690_3200000_3250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000692_0_50001.pdf
data/hpc/startmrca/qc_plots/BLFC01000706_250000_500001.pdf
data/hpc/startmrca/qc_plots/BLFC01000706_750000_1000001.pdf
data/hpc/startmrca/qc_plots/BLFC01000715_0_50001.pdf
data/hpc/startmrca/qc_plots/BLFC01000715_150000_200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000718_1150000_1200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000718_1250000_1400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000726_800000_850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000729_0_150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000729_150000_200001.pdf
data/hpc/startmrca/qc_plots/BLFC01000730_900000_1000001.pdf
data/hpc/startmrca/qc_plots/BLFC01000732_1950000_2000001.pdf
data/hpc/startmrca/qc_plots/BLFC01000734_350000_400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000734_800000_850001.pdf
data/hpc/startmrca/qc_plots/BLFC01000745_1250000_1300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000745_1350000_1450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000745_1600000_1650001.pdf
data/hpc/startmrca/qc_plots/BLFC01000745_300000_400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000756_600000_650001.pdf
data/hpc/startmrca/qc_plots/BLFC01000763_350000_400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000765_100000_300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000770_1200000_1250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000770_2800000_2900001.pdf
data/hpc/startmrca/qc_plots/BLFC01000770_3100000_3150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000770_650000_700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000770_850000_900001.pdf
data/hpc/startmrca/qc_plots/BLFC01000773_1700000_1750001.pdf
data/hpc/startmrca/qc_plots/BLFC01000773_2100000_2250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000773_500000_550001.pdf
data/hpc/startmrca/qc_plots/BLFC01000774_1650000_1700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000778_700000_800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000778_750000_800001.pdf
data/hpc/startmrca/qc_plots/BLFC01000816_400000_450001.pdf
data/hpc/startmrca/qc_plots/BLFC01000818_2100000_2150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000820_1050000_1100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000827_1250000_1300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000834_1200000_1250001.pdf
data/hpc/startmrca/qc_plots/BLFC01000834_3350000_3400001.pdf
data/hpc/startmrca/qc_plots/BLFC01000834_3550000_3600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000838_1750000_1950001.pdf
data/hpc/startmrca/qc_plots/BLFC01000838_550000_600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000847_1200000_1350001.pdf
data/hpc/startmrca/qc_plots/BLFC01000850_1200000_1350001.pdf
data/hpc/startmrca/qc_plots/BLFC01000857_0_100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000857_0_150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000857_650000_700001.pdf
data/hpc/startmrca/qc_plots/BLFC01000889_250000_300001.pdf
data/hpc/startmrca/qc_plots/BLFC01000909_50000_100001.pdf
data/hpc/startmrca/qc_plots/BLFC01000927_850000_900001.pdf
data/hpc/startmrca/qc_plots/BLFC01000928_550000_600001.pdf
data/hpc/startmrca/qc_plots/BLFC01000954_1100000_1150001.pdf
data/hpc/startmrca/qc_plots/BLFC01000954_750000_800001.pdf
# radseq_check
data/hpc/radseq_data/02_map_reads.sh
data/hpc/radseq_data/03_prepare_regions.sh
data/hpc/radseq_data/04_freebayes.sh
data/hpc/radseq_data/05_filter.sh
data/hpc/radseq_data/06_relatedness.sh
data/hpc/radseq_data/out.relatedness2
data/hpc/radseq_data/allrad_merged.vcf