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This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
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bcftools annotate fail to mark sites by bed file #1989

Closed ruslan-abasov closed 1 year ago

ruslan-abasov commented 1 year ago

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 commented 1 year ago

Thank you for the issue and the test case, this should be fixed now in https://github.com/samtools/bcftools/commit/40aa67d13365e2177d507d96dd97b6745503bf7b

tuncayseker commented 10 months ago

Hello.

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

Thank you