VCF conservation into Treemix
1
0
Entering edit mode
3 months ago
reza ▴ 300

I have a multi-sample vcf file with ~7 millions SNPs. Now I want to convert it into required format of the Treemix. I run it using vcf2treemix.sh along with plink2treemix.py, but plink2treemix.py works very very slow. So that if I use it, the analysis in question may take more than a month or even longer.

Does anyone of you have a solution to increase the speed of this program or a better suggestion to do this analysis

Thanks

Treemix Plink VCF • 351 views
ADD COMMENT
0
Entering edit mode

I found the solution

population program from Stacks package

ADD REPLY
0
Entering edit mode
3 months ago
sure ▴ 100

It looks to me like a custom script, and without looking at the script code, it is difficult to suggest any solution. Would it help if you split your original VCF file into chromosome VCF files and then run your code on individual chromosome files and consolidate the output in single file?

ADD COMMENT

Login before adding your answer.

Traffic: 1588 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