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Old 12-15-2011, 06:53 AM   #1
Location: long island

Join Date: May 2011
Posts: 22
Unhappy help! samtools gave me more than 500,000 snps

Dear all
I must admit that I'm a newbie in the snp calling practice. I used samtools in my analysis trying to identify SNPs from 3 human samples (belong to the same group)
I used the example code from samtools mpileup synopsis and modified it to suit my computational environment. However, the final output vcf file gave me more than 500,000 identified SNPs which really puzzled me. Then I tried it on a single sample, samtools got me more than 70,000 snps this time.

Is this normal?

Should I merge all 3 samples before I run samtools or I just treat them separately in samtools mpileup code?

Thanks a lot

Last edited by slowsmile; 12-15-2011 at 08:36 AM. Reason: asked a stupid question initially
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Old 12-15-2011, 08:24 AM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

A conservative estimate of the number of SNPs with >5% prevalence in the human genome is 10-50 million. Your observations are consistent with this:

If you go for lower prevalence, you get higher numbers. There was one suggestion passed around in a HapMap course I attended that if you sequenced the entire human population, practically every base would be a SNP (if a single observation would be good enough for validation).
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