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calculate ti/tv ratio in WGS data

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
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updated by davidc • davidc • written by chengyi31000 • chengyi31000

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.

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written by microfuge microfuge

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

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written by chengyi31000 • chengyi31000

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

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written by trausch trausch

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

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written by chengyi31000 • chengyi31000

2 answers 

bcftools stats snv.vcf.gz | grep "TSTV"
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written by trausch trausch

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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written by davidc • davidc

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