Question: How to extract fasta from 1000 genomes?
gravatar for mgrcprof
8 months ago by
mgrcprof20 wrote:

Hi there!

I'm interested in obtaining the consensus sequence for a determined chromosome in fasta format from the 1000 genomes data. I have bee looking the .bam files that the FTP site provides for each individual (whole sequencing data), however, i am interested in a determined chromosome sequence and not in the complete genome. My questions are:

Does exists a way to download a specific region of the genome data from 1000 genomes project (i suppose in .bam format)?

How can i transform a .bam file into the consensus sequence in a .fasta format?


bam 1000 genomes fasta • 379 views
ADD COMMENTlink written 8 months ago by mgrcprof20

You can use samtools to make a consensus of your bam file.

See e.g., previous posts:

How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?

ADD REPLYlink written 8 months ago by b.nota3.6k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1360 users visited in the last hour