I'm trying to run Torrent Variant Caller but run into an error
ERROR: Reference in BAM file does not match fasta file Chromosome chrMin BAM has length 16569 while fasta has 16571
that fasta is my reference fasta. I'm stuck and don't know where to go from here. So far what I've tried is converting the BAM to FASTA with samtools fasta and grepping for ">" to get all the sequence identifiers. Problem is they all look like
>CPC1U:05872:00580
I've looked around for the samtools file that does this conversion so that I can try to deduce what these IDs mean and hopefully find which ones make up chromosome M. Probably not the quickest solution, but I would be very appreciative to hear others' ideas.
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Hello stphnwist!
Questions similar to yours can already be found at:
(you're using a wrong REFerence genome, use the one that was used to map the BAM files)
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!