This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Algorithm to find PL indicies containing a specific allele

I'd like to find all of the PL indices in a VCF line for a specific allele at sites with an arbitrary number of alleles and arbitrary sample ploidy. For dipolid samples, the algorithm is straightforward, but things get more complicated for plodies 3 and above. The related question of finding the PL index given a genotype already has a nice algorithm http://gatkforums.broadinstitute.org/gatk/discussion/2157/gatk-vcf-pl-field-ordering-for-pooled-polyploid-samples.

I already have some code to do this (see below), but it's not very elegant. Does anyone have a better algorithm?

vcf sequencing algorithm
• 2,243 views • link
updated by Ram Ram • written by donfreed donfreed

1 answer

I was able to come up with a solution and I have updated the gist with a recursive function, non-recursive function and profiling of the results. I am posting here in case anyone finds the code useful.

Now only if I could figure out how to embed the gist...

• 1 views • link
written by donfreed donfreed

Log in to answer this question.

More posts like this