Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Want to make NGS libraries from single-stranded DNA or ancient DNA? BioDynami Vendor Forum 0 05-21-2018 05:09 PM
Ancient DNA Samples GraemeFox 454 Pyrosequencing 0 09-16-2012 11:58 PM
Ancient DNA adaptor removal and read merging jimmybee Bioinformatics 8 05-24-2012 07:40 PM
Ancient DNA in Maryland odile Introductions 0 11-05-2009 10:17 AM

Thread Tools
Old 04-05-2019, 10:40 AM   #1
Junior Member
Location: Montana

Join Date: Apr 2019
Posts: 1
Default Help with ancient DNA consensus

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)
genesandbones is offline   Reply With Quote
Old 04-09-2019, 12:26 AM   #2
Location: Louisiana

Join Date: Nov 2013
Posts: 38

You might be able to find some more resources on your bcftools pipeline on Just query for bcftools variant calling or something to see if you can find more resources.
Gopo is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 01:16 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO