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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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Issue generating GC correction file #103

Closed dsampath31 closed 3 years ago

dsampath31 commented 3 years ago

Hi,

I am trying to run WES tumor BAMs through ASCAT. So far, I have used sarek and ascat documentation to create BAF and logR inputs. I have issues in creating .gc file. I am using 1000G VCF and the script GCfilecreation.sh complains on bedtools nuc step to generate the output. Could you possibly help with this? or is there a .gc file somewhere for GRCh38 that I could use?

Thanks

keiranmraine commented 3 years ago

Although you have closed this I will reiterate the note at the top of the README. WES (aka WXS) is not supported via this set of wrapper tools, only WGS.