SOLiD annotations in SAM/BAM output

[adameur]

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

[svl]

The pileup command in SAMTOOLS can be used for generating position-based output and consensus/indel calling.
http://samtools.sourceforge.net/pileup.shtml

update:
I now realize you probably mean something else, the column with "a comma-separated string representing annotations on the sequence". In that case you better find someone that uses Bioscope

-Stef

[adameur]

Yes, that's the annotation string I'm looking for. I should have been clearer in the original post, sorry for that.

/Adam

[KevinLam]

do u still have the old bioscope installer?
it installs locally quite alright.
there's this python script
./corona-1.0.1r0-4/bin/mates2gff.py

Not too sure but suspect its what you need to convert ma file to gff

#!/usr/bin/python
__doc__="""
Converts a mates file to a GFF file for visualization in Apollo.
"""
import sys

class Mates2Gff( CommandLineApp ):
"""
Converts a mates file to a GFF file for downstream analysis and visualization.

[adameur]

Thanks, I tried the old bioscope code but failed to run the gff conversion..

But now I have an alternative solution. I modified the .ma header lines to match the output produced by corona_lite and then ran the old versions of MaToGff.sh and AnnotateChanges.sh. I know it's an ugly fix but at least it seems to work