This repository was archived by the owner on May 15, 2020. It is now read-only.
This repository was archived by the owner on May 15, 2020. It is now read-only.
Open
Description
Hi,
In the latest version 1.38 when I am running Somatic-WGS workflow, it is expecting a ploidyVcfFile at the 5th step 'CanvasPartition'.
So the command has:
${DOTNET}/dotnet {$CANVAS}/CanvasPartition/CanvasPartition.dll -p ""
So instead of NULL the script is taking it as an empty string and still trying to validate the VCF and erroring out.
Can you please check if that is actually an issue?
The way I am running CANVAS is:
{$DOTNET}/dotnet {$CANVAS}/Canvas.dll Somatic-WGS
--bam=$TUMOR_BAMFILE
--output=$outdir
--reference=$CANVAS_data/kmer.fa
--genome-folder=$CANVAS_data/WholeGenomeFasta
--sample-name=$SAMPLE
--filter-bed=$CANVAS_data/filter13.bed
--sample-b-allele-vcf=$NORMAL_VCF
--somatic-vcf=$TUMOR_VCF
Metadata
Metadata
Assignees
Labels
No labels