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Hello,
I hope this is the correct place to put this. I'm new here. I'm also pretty new at bioinformatics and have only self-taught my self what I know so far.
I've been trying to obtain a consensus sequence via the command line. I'm using bwa for mapping, samtools for various viewing/filtering/sorting, then bcftools mpilupe, calls, and consensus.
My problem is that the consensus is basically just spitting out the reference sequence (the human mtDNA rCRS in this case). I have been searching the internet for hours for help and it's either not relevant to aDNA or its beyond my bioinformatics knowledge.
I've attached my short basic script.
I really appreciate any help with this!!
I hope this is the correct place to put this. I'm new here. I'm also pretty new at bioinformatics and have only self-taught my self what I know so far.
I've been trying to obtain a consensus sequence via the command line. I'm using bwa for mapping, samtools for various viewing/filtering/sorting, then bcftools mpilupe, calls, and consensus.
My problem is that the consensus is basically just spitting out the reference sequence (the human mtDNA rCRS in this case). I have been searching the internet for hours for help and it's either not relevant to aDNA or its beyond my bioinformatics knowledge.
I've attached my short basic script.
I really appreciate any help with this!!
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