Question: How do I call somatic indels from a VCF file?
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gravatar for AcademicDialysis
2.4 years ago by
United States
AcademicDialysis70 wrote:

Hi,

I'm doing an analysis to find Indels in a cancer sample. I've used Platypus to call variants and VCF tools to filter out all variations except indels. I have matched normal exome data, and the recommendation is to call the indels on both the tumor and normal sample at the same time against the reference genome (hg38 in my case), then use the somaticMutationDetector.py script to call the actual mutations based on the VCF output from Platypus. In trying to run that extension script, I get the error:

Could not find normal sample normaldna in input VCF header

I get the same error with the tumor sample. I've tried the original file name (normaldna.bam), the file name without the extension (normaldna), and the full file path (/dir/that/contains/normaldna.bam). I already looked through the VCF input file, and I can't find where it is supposed to specify the original BAM a particular indel was called for. Does anyone know of any other post-processing tool of a VCF I could do to accomplish this, or have any experience with this script in particular? I know there are dozens of indel callers, but I'm pretty set on Platypus.

cancer platypus mutation indel vcf • 998 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by AcademicDialysis70
2

Update: You can see Andy Rimmer's answer to this question on the Google Group for Platypus here:

https://groups.google.com/forum/#!topic/platypus-users/1kIfOBDfkfA

ADD REPLYlink written 2.4 years ago by AcademicDialysis70
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