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DEploid-dev / DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
http://deploid.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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extract plaf from vcf #142

Closed shajoezhu closed 3 years ago

shajoezhu commented 8 years ago

Extract AF from VCF

eg.

AC=22;AF=0.012;AN=64;

dcm9123 commented 5 years ago

Hi! I am new to DEploid and I am currently trying to figure out different haplotypes across a set of patients from Ethiopia. I was wondering if there's a way of extracting the plaf file from a vcf file, given that I do not have with me the population level of the strains. Is that possible?

thanks!

shajoezhu commented 5 years ago

Hi @dcastaneda5 , I have a separate script to extract all # of ALT and all # of REF at the site j, and compute PLAF as sum(ALT)/sum(ALT+REF) over all samples. Been meaning to include this operation into the program, just haven't got around to do it. In some VCF files, PLAF is already given, I assume this is not the case for you?

dcm9123 commented 5 years ago

I see. No, in my vcf file I am not getting the PLAF that is needed. Is there any way I can extract it?

Many thanks!