Entering edit mode

6 weeks ago

rheab1230
▴
20

Hello everyone, I have vcf files for chr 1 to 22. I want to do a summary statistics for these vcf files. Like find out the sample size, no. of SNP,mean and standard deviation. Is there any software or tools which can plot graph for these calculations? Thank You.

You should mention that you've tried the vcfstats software and are facing issues; and also point to your post: error related to vcfstats

Yes, I tried vcfstats but its showing error. So now I am trying bcftools stats and then plot-vcfstats to analyse the output produce by bcftools stats. But its showing error the error:

Install

`matplotlib`

: https://matplotlib.org/stable/users/installing.htmlThank you so much. I am able to do it now. I installed matplotlib

I got this as summary:

I am not really able to understand how to get information from this summary? Like what does n or ts/tv means. Like what does this summary overall predict?

ts/tv is the ratio between transition/transversion, see for instance here: Ti Tv ratio and their usefulness in exome sequencing n is the number of SNPs (2893523) or indels (109293) I think.