How is SNP quality calculated in SAMTOOLS pileup?

[lazyworm]

Hi all,
I just wonder how is SNP quality (column 5) in SAMTOOLS pileup file calculated. I have googled for a long time without success. If you know where I can find a clear description about SNP quality, please tell me!

Thanks

[nilshomer]

Hi all,
I just wonder how is SNP quality (column 5) in SAMTOOLS pileup file calculated. I have googled for a long time without success. If you know where I can find a clear description about SNP quality, please tell me!

Thanks

Take a look at the supplementary materials in the MAQ paper (Li et al.). SAMtools uses the MAQ SNP calling model.

[kajsa]

Another question about good quality SNP calling

Hello everybody,

I have a similar question about good quality SNP calling.

I have an MOSAIK assembly with Solexa 35 bp reads with quite low coverage (ranging between 0-15X). I am planning to use the SAMtools pileup -c output to extract high quality SNPs.

I'm thinking of using the last column with the quality for each base in that position for filtering out the SNPs with good base quality.

Here is my question: If I want to be really sure about the quality of an SNP where it is low coverage: Should I use the SNP quality in column 6 or the quality for each base at column 10?

What do you think?

Regards Kajsa