VCF file CSQ flag

Question

[Payal]

Hello,

I am new to exome sequencing. I ran GATK4 and have a g.VCF file. I used VEP to annotate the gVCF file. I have a couple of questions.

1. I noticed not all the rows(variants) have the CSQ flag. Is that normal? Or I missed something? [I used --coding_only in VEP along with other options]
2. What the main things to look for in a vcf file to get meaningful information out of the vcf file and what tools to use for that? [I don't have a specific list of genes to look for right now]

Thanks,
Payal

[Ram]

a g.VCF file

A .vcf file or a gvcf file?

[Payal]

Its a gvcf file

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S101    S102    S103    S104    S105    

[Ram]

A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci with an actual consequence to the variation. Since you use the --coding-only flag, the number of sites with annotations will be even fewer.

[Payal]

this makes sense

[Pierre Lindenbaum]

if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.files with CombineGVCFs and then call GenotypeGVCFs

[Ram]

True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.

[Payal]

I am sorry. I should have been clear. I actually did run CombineGVCFs and then call GenotypeGVCFs and this is my final vcf file.

[Ram]

Ignore my earlier point on gVCFs. If you ran GenotypeGVCFs, you should already have regular VCF output. However, given you used --coding-only, only coding variants will be annotated.