Question: How to extract fasta from 1000 genomes?
2
gravatar for mgrcprof
6 months ago by
mgrcprof20
Madrid/ISCII
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?

Thanks!

bam 1000 genomes fasta • 306 views
ADD COMMENTlink written 6 months ago by mgrcprof20
2

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 6 months ago by b.nota3.5k
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