How to extract consensus sequence for a genomic region from a bam file
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4 weeks 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 • 275 views
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