What does "varreads" mean in the reason.txt file after run reasoning_v1.1.py?

biosinodx / SCcaller

Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data

GNU Affero General Public License v3.0

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What does "varreads" mean in the reason.txt file after run reasoning_v1.1.py? #8

Closed MinS1 closed 5 years ago

MinS1 commented 5 years ago

Hi, there a lot of variants with 'varreads' in cell-bulk.reason.txt file, I want to know what does "varreads" mean in the reason.txt file after run reasoning_v1.1.py?

Thank you !

biosinodx commented 5 years ago

Hi, it means that there are reads reporting the same variant in the bulk bam file that you input to the reason_v1.1.py.

biosinodx commented 5 years ago

Btw, we are finalizing our new version of sccaller, in which we fixed some bugs in SNV/INDEL calling and made it much easier for users. You may see it here in the github after one or two weeks.