5 (& 8). Loci catalog - Stacks: ref_map

# bash script
# remember that Stacks needs to be run twice; first to produce a partially-filtered VCF from which we make the blacklist
# then a second time with said blacklist so that we have our fully-filtered results.

# first run

# pipeline pre-check - stacks 1, species IDing
# no filtering options because cross-species stuff will get messy
# #!/bin/bash
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=8

module load Stacks/2.5-iccifort-2019.5.281

ref_map.pl -T 8 --samples /user/gent/427/vsc42733/BumbleBeeData/sorted/ \
--popmap /user/gent/427/vsc42733/data/pop_maps/check_country.txt \
-o /user/gent/427/vsc42733/BumbleBeeData/stacks_species/ \
-X "populations:--write-random-snp" \
-X "populations:--ordered-export" \
-X "populations:--vcf" \
-X "populations:--fstats" \

# second run - after species ID and after generating a blacklist

# lapidarius
#!/bin/bash
#PBS -l walltime=06:00:00
#PBS -l nodes=1:ppn=8

module load Stacks/2.5-iccifort-2019.5.281

ref_map.pl -T 8 --samples /user/gent/427/vsc42733/BumbleBeeData/RawRADSeqData/bp_sorted/ \
--popmap /user/gent/427/vsc42733/BumbleBeeData/Analysis/stacks/lapi_subpops/lapi_subpops_pop_map.txt \
-o /user/gent/427/vsc42733/BumbleBeeData/Analysis/stacks/lapi_subpops/ \
-X "populations:--blacklist /user/gent/427/vsc42733/BumbleBeeData/Analysis/stacks/lapi/lapi_blacklist.txt" \
-X "populations:--min-samples-per-pop 0.5" \
-X "populations:--min-maf 0.05" \
-X "populations:--write-random-snp" \
-X "populations:--ordered-export" \
-X "populations:--vcf" \
-X "populations:--structure" \
-X "populations:--fstats" \