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KCCG / mity

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
MIT License
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cram for mm10 #21

Closed AhmedArslan closed 1 year ago

AhmedArslan commented 1 year ago

Hi, I know cram file supported have been added (https://github.com/KCCG/mity/issues/6) but when I am running mity on cram files for mm10 and getting the following error.

mity call --reference mm10 --prefix CH --out-folder-path CH.cram --region chrMT:1-16299 --normalise mity version 0.4.0 Calling mitochondrial variants Running FreeBayes in sensitive mode FreeBayes failed: b'ERROR(freebayes): Could not open input BAM files\nBamMultiReader::Open: unable to open all files: \t\n\tunable to open file: CH.cram\n\n'

drmjc commented 1 year ago

Hi, I've never tried this combination (of mm10 and cram), but let's start with the command. can you try:

mity call --reference mm10 --prefix CH --out-folder-path ./CH_results/ --region chrMT:1-16299 --normalise CH.cram

thanks

AhmedArslan commented 1 year ago

Thanks, it did work, eventually.