Snp Filtering After Being Called.

Question

[Bioscientist]

I'm now calling SNP using both samtools and GATK. To achieve a better specificity, I would guess: 1.Find the overlap between the two approach. (So will the # of callings of both be similar, or dramatically different?) 2.There's some other tools for filtering of SNP?

btw, I think GATK is way much much more complicated program; so I guess GATK can achieve both better sensitivity and specificity?

thx

Answer 1

[Sean Davis]

Take a look at this site as a starting place. Much of the approach will be applicable to both GATK and samtools.

http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3

[Sean Davis]

Yep. Variant calling is not for the faint-of-heart.

[Bioscientist]

THX....But just wanna say, GATK is sooooooooo complicated! It takes me > 10 steps to do realignment, fix mate pair, recalibrate, and calling SNP. And still tons of trick to filter them!

Answer 2

[Jorge Amigo]

since this question has come again to life, I should say that the best answer I've seen has been already given Difference Between Samtools And Gatk Algorithms, and that there is a short but comprehensive piece of information from the GATK deverlopers here.