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10XGenomics / vartrix

Single-Cell Genotyping Tool
MIT License
200 stars 26 forks source link

Coverage of reads when using umi mode #71

Open korakusa opened 2 years ago

korakusa commented 2 years ago

Dear developers: Thank you for the wonderful tool.

Is there any way to know the coverage of reads when using --umi mode? In umi mode, only read with UB tag is considered, so I think that the coverage is different from that in non-umi mode. Is my understanding correct?

If so, how do I know the coverage of reads when using umi mode? One way I came up with is to filter the input bam file to only the reads that have the UB tags in advance, but does this give me the result I want?

Thanks a lot in ahead.

korakusa commented 2 years ago

Dear developers,

In order to reduce calls due to sequence error, I would like to use umi mode and further filter by the number of mutant reads. Please tell me if there is a way to know the mutant read count when running umi mode.

Thank you.