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10XGenomics / vartrix

Single-Cell Genotyping Tool
MIT License
185 stars 27 forks source link

vartrix Crash Report #66

Closed sanchezy closed 1 year ago

sanchezy commented 2 years ago

Hi, I am using vartrix as part of the souporcell pipeline [(https://github.com/wheaton5/souporcell)] and got the following crash reports for 2 of my 16 samples. Could you please advice on how to go around this issue? Many thanks, report-9cf628a8-32bd-4909-89bc-3f1dae7ab1f5.toml.zip report-9e161367-2abf-4850-9291-20c770938cbb.toml.zip

sagnikbanerjee15 commented 1 year ago

Hi @sanchezy ,

Was this issue resolved?

Thanks.

pmarks commented 1 year ago

Hi @sanchezy - this is being caused by some weird alignments in your BAM file. The latest version of vartrix (1.1.22) is more permissive of these reads, and should at least give a better error message if it doesn't understand a read. Could you please retry with that version? Thanks.