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add configuration for example 1
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vasicek58 committed Feb 15, 2024

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# ---------------- Global parameters ----------------
Ensembl_FTP_URL: ftp.ensembl.org/pub/release-111/
annotationFilename: Homo_sapiens.GRCh38.111.chr_patch_hapl_scaff
ensembl_release: 111

custom_transcript_list: "data/transcripts_reference_111.csv"
included_transcript_biotypes: ""

final_fasta_file: "results/example1_concatenated_database.fa"

# ---------------- ProHap parameters ----------------
include_haplo: True

phased_FTP_URL: ""
phased_local_path: "sample_data/"
phased_vcf_file_name: "sample_chr{chr}_1kGP_GRCh38_phased.vcf"

working_dir_name_haplo: haplotypes_tmp

phased_min_af: 0.01
phased_af_field: AF
haplo_min_freq: 0
haplo_min_count: 0

haplo_require_start: 1
haplo_ignore_UTR: 1
haplo_skip_start_lost: 1
max_cores: 1

haplo_fasta_file: "results/example1_haplotype_translations.fa"
haplo_table_file: "results/example1_haplotypes.tsv"

# ---------------- ProVar parameters ----------------
include_var: False
variant_vcf: {}

working_dir_name_var: variants_tmp

var_require_start: 1

var_fasta_file: ""
var_table_file: ""

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