I have recently gotten Absolute working with whole exome sequencing data, but I really wanted to use the information present in phasing allele specific copy number ratios that Hapseg gives to help out with the identifiably problem (multiple similar solutions, for example see http://bioinformatics.oxfordjournals.org/content/early/2014/04/21/bioinformatics.btu174.abstract). Rather than giving up and using a different tool, I was wondering if anyone has had success using HapSeg+Absolute with WES input, or doing something similar to prepare WES data for Absolute in a similar phased haplotype specific CNA way for Absolute as input? I really like how Absolute includes a prior over various known karyotypes in it's likelihood model, which I haven't seen in other methods yet.
Thanks!
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John St. John
1 answer
Although the algorithm is in beta, you can try AllelicCapseg. Contact CGA at recapseg@broadinstitute.org, and ask to be directed to the AllelicCapseg download page. AllelicCapseg segments sequencing data, including whole exome sequences, in a manner that is sequencing platform independent. The AllelicCapseg to ABSOLUTE workflow is recommended for sequence data.
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Would you mind posting the steps it took to get Absolute running on your WES samples?
I second Christian's request. If I get it running, maybe I can answer your question :-)
Have you tried this version of CapSeg by Aaron McKenna?
Have you succeed in purity and ploidy estimateing on WES data ?