Question: Algorithm to find PL indicies containing a specific allele
0
gravatar for donfreed
3.9 years ago by
donfreed1.5k
Mountain View, CA
donfreed1.5k wrote:

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?

https://gist.github.com/DonFreed/7be49091b4fd998bc9a4

sequencing algorithm vcf • 915 views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by donfreed1.5k
1
gravatar for donfreed
3.9 years ago by
donfreed1.5k
Mountain View, CA
donfreed1.5k wrote:

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...

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by donfreed1.5k
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