How to visualize gVCF?

Question

[Annika Forsingdal]

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

[WouterDeCoster]

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.

[Pierre Lindenbaum]

duplicate of Best visual and interactive genotype matrix (VCF) exploration tool

[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?

[Pierre Lindenbaum]

as far as I know gvcf ( https://sites.google.com/site/gvcftools/home/about-gvcf / https://software.broadinstitute.org/gatk/guide/article?id=4017 ) are VCF.

[Myo Naung]

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

Answer 1

[ning]

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.