calculate ti/tv ratio in WGS data

Question

[chengyi31000]

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.

[microfuge]

ts/tv ratio is important for judging the overall quality of your calls. It should not be too different from known values for your species. I usually employ it as one of the gold standards to reach while filtering.

[chengyi31000]

how can i determine the standards of ts/tv ratio? How can I filtering?

[trausch]

The expected ratio of transitions to transversions in the whole genome is near 2.0 for humans.

[chengyi31000]

Is it meaningful to calculate ti/tv ratio by each chromosome ? or it must calculate ti/tv ratio by all chromosome

Answer 1

[trausch]

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

Answer 2

[davidc]

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.