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cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
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Using chromosome reference in Scomatic #62

Closed Arsamat closed 3 months ago

Arsamat commented 3 months ago

Hi,

I was running SComatic on single-cell data that I have. In the example, chr10 from grch38 was used as a reference. However, if I were to also see mutations in other chromosomes would I have to rerun step 4 separately for each chromosome with its respective grch38 reference? Thank you!

ArthurDondi commented 3 months ago

Hi, you could run it again from step 2 with the complete hg38.fa reference (available here https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) with --chrom all .

You can also run each chromosome separately, but from step 2, not step 4 (the BaseCellCounter file is already filtered).