Creating Pyclone-VI input file from ASCAT and Strelka2 tool outputs

[sreerampeela]

Hi, I am currently trying to use Pyclone-VI for identifying subclones within cancer bulk genome sequence datasets. I created a segments file using 1000G loci and allele files as recommeded in ASCAT, and used strelka2 tool for somatic variant calling. The SNVs from strelka2 are further filtered for min. DP = 5, FILTER = PASS, MAPQ >30. Following this, I have the below queries:

1. In case of assigning copy numbers (major and minor), if a variant spans the loci in segment file, I can use the major_cn and minor_cn for the variant. In case a variant does not span a segment (ASCAT), should these be similar to the WT CNA (major = minor = 1)?
2. If some set of variants span a segment, can I use the major and minor copy numbers of the entire segment for all the variants?
3. Should we use only biallelic SNPs or all variants have to be included?
4. Can we use germline variants in the Pyclone-VI analysis? Some of my downstream analyses should include germline variants too.
5. How much should the average depth be for calling a binomial/beta-binomial model, if the number of tumor samples = 7 and one normal sample?
   Any clarification regarding this can greatly help my research. Thank you.