PureCN
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lima1
Suggest allowing multiple samples in VCF file.
Suggestion: add arg to specify normal sample ID also. Then, allow the VCF file to contain more than two samples. In my case with multiregional sequencing, the easiest way for me to make an appropriate VCF for PureCN is to make one that has all samples of a person, one normal and multiple tumor samples. I would run PureCN once for each tumor sample, specifying the same VCF each time, the same normal sample ID, and a different tumor sample ID.
No problem. I had actually made a vcf with only two samples, but it had all my samples in it. Discovered that bcftools annotate -s option does not work, reported it as bcftools bug.
I hope to have a finished PureCN run on all my samples today, with new VCF files made using the same variants as we are using in the rest of the project, which is SNVs called by multiSNV and indels called by Mutect2. I’m plotting all the PureCN output info for all my samples, I’ll send you a plot pdf when I get one, just in case you want to take a look at the output on files from a different project.
We’ve already determined from PureCN that our purity is lower than we expected, although this isn’t surprising because it is diffuse gastric cancer, diffuse meaning there tends to be few tumor cells amongst many normal cells. So, we are moving forward with doing more sequencing to get greater depth.
ted
— Ted Toal, Postdoctoral Researcher Carvajal-Carmona Lab Dept. of Biochemistry and Molecular Medicine 4502 GBSF, One Shields Ave Davis, CA 956626 (530) 263-5986 [email protected]
On May 14, 2018, at 10:04 AM, M. Riester [email protected] wrote:
Thanks Ted for adding this to the tracker. This might take a while though.
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