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Old 04-05-2019, 10:40 AM   #1
genesandbones
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Location: Montana

Join Date: Apr 2019
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Default Help with ancient DNA consensus

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!!
Attached Files
File Type: txt basic_pipeline copy.txt (1.8 KB, 2 views)
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Old 04-09-2019, 12:26 AM   #2
Gopo
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Location: Louisiana

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You might be able to find some more resources on your bcftools pipeline on www.biostars.org. Just query for bcftools variant calling or something to see if you can find more resources.
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