gVCF size human genome

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2.8 years ago

quentin54520 ▴ 120

Hello all,

I got some gvcf using haplotypecaller in gvcf mode (-ERC GVCF). In input I am using human genomes, at around 35 / 40x. I wanted to know what is the classic size of such a gvcf? I ask that because I have a few between 17 and 21Go, but on the other hand another one is at 8.6Go. Haplotypecaller finished without generating any errors so I guess everything is okay but to be honest I don't know how to be sure it's okay.

Thanks in advance.

variant Gatk gvcf • 1.1k views

ADD COMMENT • link 2.8 years ago by quentin54520 ▴ 120

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Using file sizes is not a reliable metric for most anything except making sure a tool worked i.e. it produced a non-zero byte file (of a reasonable size). VCF file sizes will depend on number of variants in your files and how compressible the files are.

ADD REPLY • link 2.8 years ago by GenoMax 141k

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Yes I'm agree, I did not know of any tools allowing to check the quality of my gvcf (or in any case if they are consistent).I finally used CollectVariantCallingMetrics and I get consistent snp numbers in the different samples.

ADD REPLY • link 2.8 years ago by quentin54520 ▴ 120

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