Question: calculate ti/tv ratio in WGS data
0
gravatar for chengyi31000
11 months ago by
chengyi3100010
chengyi3100010 wrote:

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 • 891 views
ADD COMMENTlink modified 11 months ago by trausch1.2k • written 11 months ago by chengyi3100010
1

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.

ADD REPLYlink written 11 months ago by microfuge1.0k

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

ADD REPLYlink written 11 months ago by chengyi3100010
1

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

ADD REPLYlink written 11 months ago by trausch1.2k

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

ADD REPLYlink written 11 months ago by chengyi3100010
1
gravatar for trausch
11 months ago by
trausch1.2k
Germany
trausch1.2k wrote:
bcftools stats snv.vcf.gz | grep "TSTV"
ADD COMMENTlink written 11 months ago by trausch1.2k
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