1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
14 bcftools view --trim-alt-alleles $vcf | egrep -v "\*|<NON_REF>" | tee \
15 >( /gvcf_regions/gvcf_regions.py --min_GQ $gqcutoff - > "$sampleid".bed ) \
16 >( rtg vcffilter -i - -o - --remove-overlapping | awk '{if ($5 != ".") print $0}' | bgzip -c > "$sampleid"_varonly.vcf.gz ) \
19 bedtools subtract -a $genomebed -b "$sampleid".bed > "$sampleid"_nocall.bed
21 tabix "$sampleid"_varonly.vcf.gz