filters not compatible with 'chr' in chromosome identifiers. ie. requires '1' instead of 'chr1'

inab / SmartRNASeqCaller

SmartRNASeqCaller is a post-processing pipeline to improve germline variant calling from RNA-Seq data

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filters not compatible with 'chr' in chromosome identifiers. ie. requires '1' instead of 'chr1' #6

Closed brianjohnhaas closed 4 years ago

brianjohnhaas commented 4 years ago

Hi,

I noticed that if the genome being used includes 'chr' in the chromosome identifiers, the various filters aren't working, such as splice adjacency, repeat masker overlap, etc., as none of the resource files contain 'chr' identifiers and none of the resulting 'bed intersect' calls find overlaps.

Genomes downloaded from GENCODE all contain 'chr' identifiers, and this breaks compatibility.

mbosio85 commented 4 years ago

Hi,

This is a latent issue because for legacy reasons we had to deal with BAMs without the chr and basically we kept it. I resolved to update the resource folder with :

adding the chr prefix to the default files so by default the tool has compatibility with GENCODE annotation
adding a new set of files with 'nochr' in the name so that we can have the files without 'chr' in it in case it's needed.

Cheers, Mattia