How to extract consensus sequence for a genomic region from a bam file
0
0
Entering edit mode
3.0 years ago

I've been given a bam file from whole genome sequencing of a cell line. I need to extract the consensus sequence for the genomic region chr4:3075603-3077670 (GRCh37/hg19). I can display the bam in GenomeBrowser, but how to I extract the sequencing results for this region? I've dabbled with samtools, using the commands 'view', 'fasta', and 'faidx', but can't work out how to get the sequence out. Thanks!

samtools bam • 1.1k views
ADD COMMENT
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 3096 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6