How to extract fasta from 1000 genomes?
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!
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martingarridorc •
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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?