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Some variants have ./. genotype with no read depth info in VCF file

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

sequencing
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written by barslmn • barslmn

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.

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written by Devon Ryan Devon Ryan

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