plot-vcfstats
1
0
Entering edit mode
6 weeks ago
rheab1230 ▴ 20

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 • 495 views
ADD COMMENT
0
Entering edit mode
6 weeks ago
samuelandjw ▴ 120

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1293 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6