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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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[ERROR]cobalt germline error #432

Closed YuP9934 closed 10 months ago

YuP9934 commented 12 months ago

hi,I only have a standard sample data of NA12878, and I want to run purple software to detect copy number variation. So I've chosen the germline mode.But I had a problem executing it.Could you help me deal it? When I use cobalt, the script I use is '_java -jar cobalt_v1.14.jar -reference WGS -reference_bam WGS.bam -gc_profile GCprofile.1000bp.37.cnp' But there was a mistake, ERROR:'Warning: pcf is not run for sample 1 on chromosome arm because all observations are missing. NA is returned.' I don't know. Is there something missing in my input? Without the pcf file, the purple behind it will not work properly

p-priestley commented 12 months ago

Just to be sure of your use case, PURPLE is not intended as a comprehensive germline CNV caller. The germline mode is mainly to annotate germline SV and SNV with the correct copy number and to identify genes that are deleted in the germline.

hongwingl commented 12 months ago

Cobalt expect chromosome names for v37 to be 1, 2, 3.. X, Y etc. What is the chromosome names for NA12878 bam file? You can find that with samtools view -H WGS.bam