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3.6 years ago
michael.flower.14
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200
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!
See this: Generating consensus sequence from bam file