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How to visualize gVCF?

Dear Biostars community,

How can gVCF files be visualized? Can I use IGV as with VCF files? Do you have any recommendations for working with gVCF files?

Thanks, Annika

gvcf
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updated by ning • ning • written by Annika Forsingdal Annika Forsingdal

Thanks for this comment. The post you are referring to is about VCF files, does all the same applies to files in gVCF format?

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written by Annika Forsingdal Annika Forsingdal

i think gvcfs are the likelihood of variants so that we can do joint genotyping, and variant calling

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written by Myo Naung • Myo Naung

I obviously don't know why you want to visualise your gVCF files, but I would think you need to do further processing (variant calling: GATK GenotypeGVCFs) to make the results meaningful.

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written by WouterDeCoster WouterDeCoster

1 answer

IGV works with GVCF files. The only caveat is that you have to use a ".g.vcf" extension rather than a ".vcf" extension (or ".g.vcf.gz" rather than ".vcf.gz").

Re "why you want to visualise your gVCF files": I think it's a good idea to visualise intermediate results as a sanity check. For example, if my data came from exome sequencing, then I would expect IGV to show gVCF records concentrated in exonic regions.

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written by ning • ning

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