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ld_pruning.wdl
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ld_pruning.wdl
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version 1.0
import "variant_filtering.wdl" as variant_tasks
import "https://raw.githubusercontent.com/UW-GAC/primed-file-conversion/main/plink2_pgen2vcf.wdl" as pgen_conversion
workflow LD_pruning {
input {
Array[File] vcf
File? variant_file
Int? variant_id_col
Float? min_maf
Boolean? snps_only
Int? window_size
Int? shift_size
Int? r2_threshold
}
scatter (file in vcf) {
call variant_tasks.subsetVariants {
input:
vcf = file,
variant_file = variant_file,
variant_id_col = variant_id_col,
min_maf = min_maf,
snps_only = snps_only
}
call variant_tasks.pruneVars {
input:
pgen = subsetVariants.subset_pgen,
pvar = subsetVariants.subset_pvar,
psam = subsetVariants.subset_psam,
window_size = window_size,
shift_size = shift_size,
r2_threshold = r2_threshold
}
call pgen_conversion.pgen2vcf {
input:
pgen = pruneVars.out_pgen,
pvar = pruneVars.out_pvar,
psam = pruneVars.out_psam
}
}
output {
Array[File] pruned_vcf = pgen2vcf.out_file
}
meta {
author: "Stephanie Gogarten"
email: "sdmorris@uw.edu"
}
}