Mitochondrial shifted reference
AnsweredHi there,
I have a question about the Mitochondrial short variant discovery documentation. In the "Align the unmapped BAM file with the reference aligned BAM and shifted reference aligned BAM" step, I don't understand which is the shifted reference BAM. Do we have to create a new reference and map against it? If so, how do we create the shifted reference?
The input required is only a BAM aligned against the full genome, isn't it?
Maybe it's something obvious, but I can't see it, I'm sorry.
Many thanks!
Marc
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The best practices article is based off our featured WDL workflow, which can be found on dockstore.
For an easy readability example, it's also on the Terra platform. We have all the resources listed there and if you have human data, you can use the shifted reference from there. Terra link: https://app.terra.bio/#workspaces/help-gatk/Mitochondria-SNPs-Indels-hg38
If it's not human, the GATK tool to create the shifted reference is ShiftFasta.
Let me know if you have any further questions.
Best,
Genevieve
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Many thanks, Genevieve!
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Hi there,
I'm using hg19 and wondering how may i create the shifted chrM fasta? Thank you so much for the kind help.
Best regards,
Michelle
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Thank you for your post, Michelle Lian ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
Please see our Support Policy for more details about how we prioritize responding to questions.
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