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Old 04-19-2017, 12:05 AM   #1
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Location: London

Join Date: Nov 2011
Posts: 3
Default Missing genotype data in .vcf file

Hi all,
I'm trying to gather genotype data from .vcf files generated using GATK (as part of Illumina's MiSeq Reporter software), but I'm getting odd results.
I'm looking at one variant site, and for individual sample vcf files, I get data when there is a variant (i.e. not homozygous reference) so that's fine.
I'd like to be able to output the data for the hom ref samples - i.e. depth at the site so I can quickly confirm whether the genotype is real (is it really homozygous reference, or a no call?).
I'm looking at the genome vcf files to get this data and for some sites I get a 0/0 call, but for others there is just a "." and when I look at the samples in IGV, the coverage is almost the same at both sites. So, I'm wondering how I can get the info that I want, and also why I would get a 0/0 genotype with all the associated info (GQ, MQ, DP, DPF etc) for some positions and not for others?
I've had a look through previous threads, but can't find any info on this.
Apologies also for my ignorance, I am a complete bioinformatics novice.
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