calculate ti/tv ratio in WGS data

2

I am dealing with WGS data with vcf files.
Wondering is it necessary to calculate ti/tv ratio to do QC?
Can I calculate ti/tv ratio using vcftools?
I have only see the function in Variants tools, but it is not that convenience to upload the big data.


sequencing


ti/tv ratio

• 3.0k views

bcftools stats snv.vcf.gz | grep "TSTV"

snpSift tstv my.vcf.gz

gives individual tstv values for each samples in a multi sample vcf and takes into account the genotype when calculating

I believe bvcftools counts the chr/pos/ref/alt but if the genotype is 0/0 still counts it.


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