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OpenGenomics / muse-tool

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MUSE compatibility with hg38 reference? #6

Open W4RJ4 opened 6 years ago

W4RJ4 commented 6 years ago

Hi, I recently tried running MuSE with hg38 reference and appropriate hg38 dbsnp database. After 10 hours I got segmentation fault(core dumped) on chr 10. And what i want to ask here is, if I made a mistake by running it at all with hg38 or there is maybe another reason why error occurred on this region?

buchanae commented 6 years ago

@W4RJ4 I can't think of why MUSE would be specific to one reference. @kamichiotti are you running your analysis on hg38?

kamichiotti commented 6 years ago

@buchanae @W4RJ4 I have been using hg19, but there shouldn't be any reason it wouldn't work on hg38 provided the files are correctly formatted and compressed. The error may be due large input BAM, particularly WGS. In this case, implementing the -r (single region (chr:pos-pos) where somatic mutations are to be called; STRING) or -l (list of regions (chr:pos-pos or BED) where somatic mutations are to be called, one region per line; FILE) options.