Using VARiD for pooled samples

[Garfield]

I have an issue. The long story can be found here:

http://seqanswers.com/forums/showthread.php?t=9946


The short story is that I have RNA-seq data from POOLS of diploid
larvae. I'd like to estimate SNP frequencies (or at least identify
SNPs) using these data.

There are, thus, two issues.

1) In any pool of larvae, I have potentially many alleles for any SNP
because each pool of larvae consists of many (at least 4 if only two
parents were used) haplotypes.

2) Allele frequencies may be skewed because
a) Allelic imbalance (common issue for RNA-seq data)
b) Rare alleles in a population are also rare in the larval pool
(rather than being 50% of rare individuals).

How does VARiD handle these situations?

Thanks,

David

[Michael Brudno]

Unfortunately this is not something that VARiD can handle...

[David Garfield]

Thanks for the info.

I look forward to trying your program for future studies.

--DG