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Overlapping variant records

I have a VCF file with two records as follows:

20    10470839    .        TTC         T         50         PASS     ... here GT = 1/0

20    10470841    .         C           CT      50          PASS     ... here GT = 0/1

This is a valid VCF that works well with the hap.py tool. I do not understand how to interpret these two records because the second record overlaps with the first. Any help is appreciated.

Thanks!

vcf
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written by oddjobs • oddjobs

1 answer

It is possible that on one strand, there's a deletion and on the other, there's an insertion. If this is from a reliable pileup/variant caller such as samtools mpileup or GATK HaplotypeCaller, the odds that this is an algorithmic error is low (assuming this is not a repeat region)

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written by Ram Ram

I see. It makes sense if it is happening on two different strands, hence the two genotypes wouldn't be overlapping or conflicting. Here the GT fields do support what you say.

Thanks!

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written by oddjobs • oddjobs

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