Frequency distribution of base quality scores from SAM file

[VeBeKay]

Hi,

does anyone know how to get the frequency distribution of base quality scores at a particular site from a SAM file?

The idea is to check if a SNP is a "true" SNP, i.e. the reference and alternative should have similar base qual. distributions if the SNP is real.

Thanks!

[sphil]

you could pull the readnames of interest from you sam/bam file using samtools. Use those names to grep for the sequences in your fastq and check how the qualities are.

[GenoMax]

Mpileup should give you that info. See this thread: http://seqanswers.com/forums/showthread.php?t=25483

[VeBeKay]

Thanks, I think this should do!