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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
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Expected ASCAT output file missing: TUMORNAME.aberrationreliability.png #38

Closed komalsrathi closed 8 years ago

komalsrathi commented 8 years ago

Hi,

I am running ascatNgs v1.5.2 for whole-exome data. At the second step i.e. -p ascat, sometimes the .aberrationreliability.png file is not created because of which finalise fails. Do you have a work around for this issue?

Thanks a lot, Komal

keiranmraine commented 8 years ago

Although there is an option '-f' to force completion you will not get a useful profile from exome analysis.

komalsrathi commented 8 years ago

Why does it not create the aberration reliability plot for some samples?

On Wednesday, March 23, 2016, Keiran Raine notifications@github.com wrote:

Although there is an option '-f' to force completion you will not get a useful profile from exome analysis.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/cancerit/ascatNgs/issues/38#issuecomment-200259667

Komal S Rathi | Bioinformatics Engineer II, Memorial Sloan Kettering Cancer Center | rathik@mskcc.org | komalr@mail.med.upenn.edu | krathi1@jhu.edu krathi1@live.johnshopkins.edu