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Depth 0 position for platinum call

Open JunhakAhn opened this issue 4 years ago • 0 comments

Hi,

I downloaded NA12878 bam file (114G) and NA12878 VCF file from the ENA (https://www.ebi.ac.uk/ena/browser/view/PRJEB3381). As far as I know, platinum variant calls are the positions with the 'PASS' filter in VCF file. If so, I think I found weird variant positions with depth zero. For instance, chromosome 1, depth of 1-based coordinate 248,806,349 is zero. The GT of this position is 1|1 and Ref/Alt are G/A. How can this position called as platinum variant? Is there anything I interpret wrongly?

Best, Ahn

JunhakAhn avatar Jan 09 '21 05:01 JunhakAhn