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sridnona / cb_sniffer

mutation(barcode) caller for 10x single cell data
GNU General Public License v3.0
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questions #13

Open louis-jliu opened 3 years ago

louis-jliu commented 3 years ago

Hi,

I'm new to variant calling and I'm trying to learn through replicating your paper's ("A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing") result. I have a couple questions that I didn't quite understand from the paper, and I would appreciate if you can help answer here:

  1. From my understanding cb_sniffer is designed to call on variants from data with known variants of interest? If so, if I have my own data, I would have to prepare a variant file from other general mutation calling tools (e.g. DNA seq variant calling results)?
  2. Is it possible to deposit the files (bam, vcf and barcode) used in the paper for a test run of the script? Last time I checked, the bam files weren't on GEO data base yet.

Thanks in advance.

Louis

sridhar0605 commented 3 years ago

Hi @louisjrliu,

  1. yes you are correct you need to call variants from a variant caller and pass those to cb_sniffer along with bams.
  2. uploading bams are work in progress(dbGAP) we apologize that we cannot help with bams we used in the paper, however if there is some test data out there which you know off i am happy to add that(PR's welcome) to the repo.

Thanks Sid