How to run mity for custom reference of non-organism model ?

[BenAawf]

Hi Dear All

I would like to test your tool for a non-organism model where i have a custom refence of its mitochondrial genome, where i would like to test a batch of sample againt this ref:

First, I run bwa-mem2 against the ref using this cmd:
bwa-mem2 mem -t $threads -M -R "@RG\tID:${prefix}\tSM:${prefix}\tLB:${prefix}\tPL:ILLUMINA" $ref $r1 $r2 | samtools view -Sb -F 4 -q 20 -@ $threads -t ${Fai_file} -o $prefix.bam
Then, after aligning my sample here, the mity cmd I used, but I cannot fix the issue related to the correct run. Could you please help in this respec,t thanks

here my cmd :
docker run -w "$PWD" -v "$PWD":"$PWD" drmjc/mity runall --keep --prefix 151314.mity --output-dir mity_output --custom-reference-genome mito.fasta --custom-reference-fasta mito.fasta 415A.bam 413A.bam 414A.bam

Is something wrong with the command above?

[trentzz]

Hi @BenAawf,

Just wanted to check, are you getting an error when running that command? If so could you send what error you're getting?

Also as this is for a non-organism model, mity report may not have a lot of useful information.

Thanks!
Trent Zeng