Summary metrics of haplotypecaller.filtered.vcf

[ojziff]

Hi @praveenraj2018

I have run nfcore/rnavar on 400 samples - it is a fantastic pipeline! Many congrats on writing and publishing this!

I want to plot summary statistics on the genome-wide variant calling output haplotypecaller.filtered.vcf files across all 400 samples and compare the diseased with healthy samples e.g. total number of variants per sample, types of variant (SNP, DEL, INS etc), the consequence of variant on protein etc. These are large VCF files and looking at each one by one is taking far too long and taking up too much memory in R.

If the pipeline could add these variant summary metrics per sample using a package like Cerebra, it would be very useful!

Many thanks!
Oliver

[praveenraj2018]

Thanks for reporting this. We will plan it for the next release.