Hi all,
not sure where to post this, so I'll put it under general.
I am checking sequences (bam files) with the IGV genome viewer, and can't figure out how to export a consensus sequence for regions containing SNPs. If I use the "define a region of interest/copy sequence" button, it copies the reference sequence for that region, not the consensus.
Is this possible in IGV; if so, how do I do that? If not, can anyone recommend a (free) bam-file viewer in which one can define (SNP threshhold etc.) a consensus and export that as a fasta or simple textfile?
Thanks in advance!
Greets
Bean
not sure where to post this, so I'll put it under general.
I am checking sequences (bam files) with the IGV genome viewer, and can't figure out how to export a consensus sequence for regions containing SNPs. If I use the "define a region of interest/copy sequence" button, it copies the reference sequence for that region, not the consensus.
Is this possible in IGV; if so, how do I do that? If not, can anyone recommend a (free) bam-file viewer in which one can define (SNP threshhold etc.) a consensus and export that as a fasta or simple textfile?
Thanks in advance!
Greets
Bean
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