1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
16 for haplotype in ${haplotypes[@]}; do
17 bcftools consensus --fasta-ref $ref --haplotype $haplotype --mask $mask $vcf | bgzip -c > "$sampleid"."$haplotype".fa.gz