MAQ and Samtools output

[dnusol]

Hi group,

I am testing samtools with my data, after having used MAQ for SNP detection.

I have found that I get a large reduction in the number of SNPs detected when using Samtools. I have read that Samtools uses the same algorithm for SNP detection as MAQ, so I guess the differences are in the filtering steps. Another difference is the use of SNP quality, which can be used for filtering, not available in MAQ output

Can anyone explain what is samtools.pl actually doing? what are the differences between options "varFilter" and "pileup2fq"?

Also I am a bit confused between these two commands
- samtools pileup (call variants and output pileup format?)
- samtools.pl pileup2fq (only transform pileup to fastq?)

I haven't found much info for the samtools.pl script

Thanks for your help,

D.