Entering edit mode
5.9 years ago
barslmn
★
2.1k
Some variants in vcf file has no read depth information and has ./. as genotype even though I can see reads there in IGV. What may be causing this?
Thanks
You can see everything in IGV, even for reads with low MAPQ and bases with low Phred scores. Have a look at both of those in IGV or at least post an IGV screenshot of an example position.