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wheaton5 / souporcell

Clustering scRNAseq by genotypes
MIT License
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Somatic variants in vcf #119

Open wenweixiong opened 3 years ago

wenweixiong commented 3 years ago

I'm interested in tracing previously identified somatic mutation for each single cell. am wondering if the souporcell_merged_sorted_vcf.vcf.gz contains only germline variants or it also contains somatic variants? If the vcf only contains germline variants, how may I tweak the pipeline to also call somatic variants?

leeheetakat commented 3 years ago

Hello, souporcell only contains germline variants which may consist of both SNP and SNV. Let's assumed that your batch contains normal and cancer samples from an individual. From the comparison between normal and cancer, you might get SNVs. When you find specific the SNV loci in the souporcell.vcf, it will be helpful to identify which souporcell cluster is cancer sample. good luck!