Hi,
here is a puzzle for VCF cracks! How do you combine 2 vcf files, where one of them has an insertion and the other one a deletion at the same position. Let's say the reference sequence is caag, the sequence of sample1 is CAG and of sample2 CAAAG. In the VCF below i skipped the columns without information for this example:
sample1:
POS REF ALT GT
1 CA C 0/1
sample2:
1 C CA 0/1
in my opinion the only correct solution would be:
1 CA C,CAA 0/1 0/2
what do you think?
here is a puzzle for VCF cracks! How do you combine 2 vcf files, where one of them has an insertion and the other one a deletion at the same position. Let's say the reference sequence is caag, the sequence of sample1 is CAG and of sample2 CAAAG. In the VCF below i skipped the columns without information for this example:
sample1:
POS REF ALT GT
1 CA C 0/1
sample2:
1 C CA 0/1
in my opinion the only correct solution would be:
1 CA C,CAA 0/1 0/2
what do you think?
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