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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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samplename not found #44

Closed Hbm3085 closed 8 years ago

Hbm3085 commented 8 years ago

Hi,

I am getting the following error while running ascat.pl :

WARN: Failed to find samplename in RG headers of /<path>/*.bam
Use of uninitialized value $sample in substitution (s///) at /apps/ascatngs/2.0.1/lib/perl5/Sanger/CGP/Ascat/Implement.pm line 280.

Is there a workaround this?

Many thanks, Hasan

keiranmraine commented 8 years ago

You need to have well formed BAM files. You can add a readgroup header to a BAM with samtools.