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caleblareau / mgatk

mgatk: mitochondrial genome analysis toolkit
http://caleblareau.github.io/mgatk
MIT License
101 stars 27 forks source link

correctly specify reference genome or .fasta file #54

Closed chrismahony closed 2 years ago

chrismahony commented 2 years ago

I am running the following:

mgatk tenx -i /mypath//atac_possorted_bam.bam \ -n Pilot1 -o Pitlo1_mgatk -c 12 \ -bt CB -b /mypath/outs/barcodes.tsv

and I get the following output:

Found file of barcodes to be parsed: /mypath/outs/barcodes.tsv Mon Jan 10 11:34:57 GMT 2022: User specified mitochondrial genome does NOT match .bam file; correctly specify reference genome or .fasta file

Any ideas? Many thanks in advance Chris

chrismahony commented 2 years ago

OK I solved this by adding the --mito-genome mm10 flag, it appears to have worked