No snp found in chrM?

[bair]

Dear All,

It's hard to find SNPs in mitochondrial by samtools default setting, like D=100. I have explored several human genome data, NA18507, SJK, Venter, Watson, no snps found in ChrM.

For Chinese han, e.g YH genome, soap found 36 SNPs in chrM, seven are novel, samtools found nothing.

Can anyone explain? Thanks

[lh3]

Don't set a maximum depth in filtering. You usually get thousands folds of coverage on chrM.

[bair]

Thanks Ih3, so your suggestion is not setting maximum depth only for chrM? Watson has ~2m SNPs got from www.jimwatsonsequence.cshl.edu, in some literature supposed >3m snps in watson, what's the reason for that? filtering ?

Thanks