How to extract consensus sequence for a genomic region from a bam file
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!
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See this: Generating consensus sequence from bam file