Question: Absolute/Hapseg on Exome (WES) Data?
3
gravatar for John St. John
6.2 years ago by
John St. John1.2k
San Francisco, CA, Cancer Therapeutics Innovation Group
John St. John1.2k wrote:

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!

ADD COMMENTlink modified 4.9 years ago by wangjq10 • written 6.2 years ago by John St. John1.2k
2

I second Christian's request. If I get it running, maybe I can answer your question :-)

ADD REPLYlink written 6.0 years ago by jeltje.van.baren80

Would you mind posting the steps it took to get Absolute running on your WES samples?

ADD REPLYlink written 6.2 years ago by Christian2.9k

https://github.com/aaronmck/CapSeg

Have you tried this version of CapSeg by Aaron McKenna?

ADD REPLYlink written 5.6 years ago by CHANG40
1
gravatar for shlee
5.1 years ago by
shlee60
United States
shlee60 wrote:

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.

ADD COMMENTlink written 5.1 years ago by shlee60

Are there any updates on the beta of AllelicCapseg? I have contacted Broad about this, but haven't heard back.

ADD REPLYlink written 21 days ago by tech0
1
gravatar for wangjq
4.9 years ago by
wangjq10
China
wangjq10 wrote:

Have you succeed in purity and ploidy estimateing on WES data ?

ADD COMMENTlink written 4.9 years ago by wangjq10
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