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raphael-group / decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
BSD 3-Clause "New" or "Revised" License
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vcf_2_decifer generating empty files #29

Closed ElizabethBorden closed 9 months ago

ElizabethBorden commented 9 months ago

Hello,

I am trying to run decifer with the output from HATCHet and a VCF file called with GATK Mutect2. I only have one tumor and one normal sample and I have checked that the sample names are consistent. I ran with the following command:

python vcf_2_decifer.py -V /xdisk/khasting/knodele/Mayo_human_data/gatk_mutect2/P1.somatic.filtered.pass.vcf -C /home/u1/knodele/Immunoediting_Human_cSCC/04_copy_number_v3_hatchet/bes -O test_P1 -M 8 -A 3 -F 0.001

But when I look through the files created they are all empty.

Do you have any suggestions?

Thanks! -Elizabeth

ElizabethBorden commented 9 months ago

Nevermind, I solved the issue, my sample was below the default purity threshold.