Hi all,
I'm trying to extract info from aligned reads in the SAM/BAM format about location of SNPs and mismatches in the reference genome. Previously I've done this through the annotated GFF files but it seems like they are not created by Bioscope 1.2. What I'm after is some equivalent of the 's' attribute in the GFF lines. I've looked at the SAM output but couldn't figure out how to extract such info. Does anyone have an idea? Or can I somehow get Bioscope to write GFFs again?
/Adam
I'm trying to extract info from aligned reads in the SAM/BAM format about location of SNPs and mismatches in the reference genome. Previously I've done this through the annotated GFF files but it seems like they are not created by Bioscope 1.2. What I'm after is some equivalent of the 's' attribute in the GFF lines. I've looked at the SAM output but couldn't figure out how to extract such info. Does anyone have an idea? Or can I somehow get Bioscope to write GFFs again?
/Adam
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