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Generate the following VCF file:
(echo "##fileformat=VCFv4.1" echo "##contig=<ID=1,assembly=b37,length=249250621>" echo "##ALT=<ID=CN2,Description=\"Copy number allele: 2 copies\">" echo "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End coordinate of this variant\">" echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" echo -e "1\t668630\t.\tG\t<CN2>\t.\t.\tEND=850204") > in.vcf
Then the following commands output the variant:
$ bcftools annotate --no-version -x INFO -Ob -o in.bcf in.vcf $ bcftools index -f in.bcf $ bcftools view --no-version -H -r 1:850204-850204 in.bcf 1 668630 . G <CN2> . . .
While the following commands output nothing:
$ bcftools annotate --no-version -x INFO -Oz -o in.vcf.gz in.vcf $ bcftools index -f in.vcf.gz $ bcftools view --no-version -H -r 1:850204-850204 in.vcf.gz
Similarly, when using INFO/END rather than INFO the output is empty again:
INFO/END
INFO
$ bcftools annotate --no-version -x INFO/END -Ob -o in.bcf in.vcf $ bcftools index -f in.bcf $ bcftools view --no-version -H -r 1:850204-850204 in.bcf
My guess is that, when bcftools annotate -x INFO is used, the command forgets to set the line->rlen field to the length of the reference allele.
bcftools annotate -x INFO
line->rlen
The text was updated successfully, but these errors were encountered:
1c3c0a9
Thank you for the bug report, this is now fixed.
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Generate the following VCF file:
Then the following commands output the variant:
While the following commands output nothing:
Similarly, when using
INFO/END
rather thanINFO
the output is empty again:My guess is that, when
bcftools annotate -x INFO
is used, the command forgets to set theline->rlen
field to the length of the reference allele.The text was updated successfully, but these errors were encountered: