Hi, guys, there is a question about the genomic gVCF file. I wonder that since gVCF contains the non-var block records, why after merge all gVCF, there are still some NA in the merged gVCF file?
And in general, how many loci can be sequenced for each sample in WES?
Thank you for your time and attention, your answer will help a lot for me!
Hi, guys, there is a question about the genomic gVCF file. I wonder that since gVCF contains the non-var block records, why after merge all gVCF, there are still some NA in the merged gVCF file?
If I understand your question correctly, why do you still see no-coverage/no-call areas even with say 100 or 1000 gVCFs merged? Well with exomes you should never pick up deep intergenic regions, for instance. So those areas will remain "NA" regardless of how many exome gVCFs you collect.
And in general, how many loci can be sequenced for each sample in WES?
30M base pairs
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Thank you for your help! I really appreciate it!
And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite puzzled. I apologize for any confusion, but may I ask why the exonic regions are not showing as '0/0' rather than "NA"? I am not referring to intergenic or intronic regions.
Thank you for your attention and time again!
can you show us an exonic position in your VCF file that is all
./.?Okay, this is the merged gVCF file.
And I confused with the file that has "./." and "0/0" at the same time. Maybe my processing pipeline is wrong in some place? That's what I mean.
the samples that are
./.have no coverage (or not enough to call a genotype) and the0/0are homozygous referenceThanks for your comment, I get it now.