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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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Including Indels in analysis #24

Open amootta opened 1 year ago

amootta commented 1 year ago

Hi, I am trying to run decifer on my variants, which includes both SNPs and indels. I am using a VCF file as input, which I am converting into the appropriate format for decifer input using the vcf2decifer script. However, the output seems to be missing all of my indels, and have excluded them out of analysis. I have checked the decifer input file as well and it seems that it has removed all my indels. Please could you let me know what is the best way to retain my indels in analysis?

Thanks