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