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plot-vcfstats

Hello everyone, Can anyone tell me how to use plot-vcfstats for many input files. I have vcf files for chr1 to chr22. I have generated test.vchk file for each chr using

bcftools stats chr1.vcf > test.vchk

I now want to use plot-vcfstats for all of these files so that i can get one graph for all the chromosomes. Can anyone please help me out with this?

bcftools snp vcf stats
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written by rheab1230 • rheab1230

1 answer

You should merge results from different chromosomes and then run plot-vcfstats:

plot-vcfstats -m chr{1..22}.vcf > combined.vchk
plot-vcfstats combined.vchk -p combined_output

All desired outputs (graph, pdf, etc.) will be in the combined_output folder.

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written by samuelandjw • samuelandjw

Hi, Yes this works. But I am trying to get the result in form of summary and graph. Like this one: This is for chr1. I want to get results like this in form of summary and graph. But when i run this command:

plot-vcfstats -m chr1.vchk chr2.vchk

I am not getting any summary.pdf file and any graph. I am just getting some numbers related to snp and indels. enter image description here

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written by rheab1230 • rheab1230

Please see my edited answer. If my answer helps you, please consider accepting it.

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written by samuelandjw • samuelandjw

Ohh Okay. I will do it and let you know if I am getting the correct output file. Thank you.

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written by rheab1230 • rheab1230

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