I hope I would be able to get some help even though my question will sound very basic, I am new to sequencing formats.
I am working on a project that involves obtaining reference sequences from the .bam files in the 1000 genomes database, to perform disease studies for a group. I used samtools view to download the genomic region I am interested in, but the actual sequence column in the .bam files seem to have reads for both forward and reverse strands. I would like to know, how I could get the simple nucleotide sequence of the reference strand from .bam file ... some kind of consensus sequence I am guessing.
I am working on a project that involves obtaining reference sequences from the .bam files in the 1000 genomes database, to perform disease studies for a group. I used samtools view to download the genomic region I am interested in, but the actual sequence column in the .bam files seem to have reads for both forward and reverse strands. I would like to know, how I could get the simple nucleotide sequence of the reference strand from .bam file ... some kind of consensus sequence I am guessing.
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