bcftools annotate fail to mark sites by bed file

[ruslan-abasov]

Hi,

I am using bcftools 1.18. I want to mark sites, that overlaps regions in bed file

vcf:
test.vcf.gz

bed:
test.bed.gz

bcftools annotate -a test.bed.gz --mark-sites +TAG -c CHROM,FROM,TO test.vcf.gz:

chr1 10611 . C G . . . GT 1/1
chr1 10623 . T C . . . GT 1/1
chr1 10647 . A G . . . GT 0/1
chr1 10671 . G C . . . GT 0/1
chr1 10676 . A G . . . GT 0/1
chr1 10705 . A G . . . GT 0/1
chr1 10729 . G C . . . GT 0/1
chr1 10734 . A G . . . GT 0/1
chr1 10751 . C G . . . GT 0/1
chr1 10758 . G C . . . GT 0/1

bcftools annotate -a test.bed.gz --mark-sites -TAG -c CHROM,FROM,TO test.vcf.gz:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test
chr1 10611 . C G . . TAG GT 1/1
chr1 10623 . T C . . TAG GT 1/1
chr1 10647 . A G . . TAG GT 0/1
chr1 10671 . G C . . TAG GT 0/1
chr1 10676 . A G . . TAG GT 0/1
chr1 10705 . A G . . TAG GT 0/1
chr1 10729 . G C . . TAG GT 0/1
chr1 10734 . A G . . TAG GT 0/1
chr1 10751 . C G . . TAG GT 0/1
chr1 10758 . G C . . TAG GT 0/1

same command, but with bcftools 1.17:

bcftools annotate -a test.bed.gz --mark-sites +TAG -c CHROM,FROM,TO test.vcf.gz

chr1 10611 . C G . . . GT 1/1
chr1 10623 . T C . . TAG GT 1/1
chr1 10647 . A G . . TAG GT 0/1
chr1 10671 . G C . . TAG GT 0/1
chr1 10676 . A G . . . GT 0/1
chr1 10705 . A G . . . GT 0/1
chr1 10729 . G C . . . GT 0/1
chr1 10734 . A G . . . GT 0/1
chr1 10751 . C G . . . GT 0/1
chr1 10758 . G C . . . GT 0/1

bcftools annotate -a test.bed.gz --mark-sites -TAG -c CHROM,FROM,TO test.vcf.gz

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test
chr1 10611 . C G . . TAG GT 1/1
chr1 10623 . T C . . . GT 1/1
chr1 10647 . A G . . . GT 0/1
chr1 10671 . G C . . . GT 0/1
chr1 10676 . A G . . TAG GT 0/1
chr1 10705 . A G . . TAG GT 0/1
chr1 10729 . G C . . TAG GT 0/1
chr1 10734 . A G . . TAG GT 0/1
chr1 10751 . C G . . TAG GT 0/1
chr1 10758 . G C . . TAG GT 0/1

[pd3]

Thank you for the issue and the test case, this should be fixed now in 40aa67d

[tuncayseker]

Hello.

This is introduced in the 1.18 version and <=1.17 versions are ok?

Thank you