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?
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