Samtools SNP quality

[dmurdock]

Hi everyone. I'm attempting to find out what goes into the samtools SNP quality calculation. I've read through the MAQ paper to no avail. I imagine it involves coverage, base quality, etc. I'm comparing snps generated by other aligners like corona lite but it's difficult to compare snp quality if I don't have a grasp of how it's calculated.

Thanks,
David Murdock

[nilshomer]

Hi everyone. I'm attempting to find out what goes into the samtools SNP quality calculation. I've read through the MAQ paper to no avail. I imagine it involves coverage, base quality, etc. I'm comparing snps generated by other aligners like corona lite but it's difficult to compare snp quality if I don't have a grasp of how it's calculated.

Thanks,
David Murdock

They are defined here:
http://samtools.sourceforge.net/cns0.shtml

Did you read the supplemental materials from the MAQ paper?