Samtools pileup SNPs questions

[Melissa]

Hi, I'm using pileup to look for SNPs from bowtie alignment. There are several questions I wanna ask. Your help is greatly appreciated.

1. I observed the maximum SNP quality is 228. Is it correct?

2. $7 is always 60. What's wrong?

3. What does the symbol "$" or "^F" means in $8?

4. Will considering a SNPs site that are covered by reads from plus & minus strand reduce false positive?

5. Also, I noticed BWA maps less reads compared to Bowtie. It gives a lower mapping score, lower SNP quality score and thus, less SNPs. Can I trust these SNPs that are found in bowtie but not BWA alignment?

Cheers,
Melissa

[lh3]

1. it depends on your data

2. in repetitive regions, you will see smaller numbers

3. see FAQ

4. see maq paper. it considers this effect, but probably not as much as it should

5. bowtie does not have a mapping score. in my evaluation, bwa always gives better alignment and better snp calls, but you know my answer is likely to be biased.

[sowmyai]

I too noticed that all most of my SNPs had quality score of 228. But I had a couple of 255s. Did you ever find out what's magical about 228 ?