bcftools consensus with deletion at POS 1 incorrect

[SoapZA]

Test script:

#!/usr/bin/env sh

cat > v.vcf <<- EOF
	##fileformat=VCFv4.2
	##fileDate=20201023
	##source=foo
	##reference=chr1
	##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
	chr1	1	del	GA	A	20	PASS	DP=100
EOF

cat > chr1.fasta <<- EOF
	>chr1
	GACT
EOF

bgzip v.vcf
bcftools index v.vcf.gz
bcftools consensus -f chr1.fasta v.vcf.gz

bcftools 1.10.2 (correct):

>chr1
ACT
Applied 1 variants

bcftools 1.11 (incorrect):

>chr1
GCT
Applied 1 variants

[pd3]

Thank you for the bug report, this is now fixed.