BWA parameters affects SNP calling with samtools?

[hellohenry]

hello everyone, I am new in using BWA and samtools, but I found something really strange: I used two different parameter settings of BWA for mapping, and I got two mapping results. Then I used samtools to call SNP from the two mapping results respectively, got SNP collection A and B. a SNP X presents in A while absent in B. But the real problem is: when I browsered the mapping results with "samtools tview", I found the locus X is a real SNP in both mapping results! So my problem is : the BWA parameter did not affected mapping results, but affected snp calling with samtools!

[hellohenry]

appreciaton

all replies are greatly appreciated!

[dpryan]

It's unlikely that the parameters you feed to bwa would change the results of SNP calling without also resulting in different mapping. In the case that you're describing, was there a difference in depth at the position in question between the SAM files? That would seem to be the most likely cause.

[hellohenry]

It's unlikely that the parameters you feed to bwa would change the results of SNP calling without also resulting in different mapping. In the case that you're describing, was there a difference in depth at the position in question between the SAM files? That would seem to be the most likely cause.

Thanks!~ I have checked the depth at the locus on both mapping results, one is 241, the other 243. So it is unlikely to be the reason....

[hellohenry]

OK, I got it, finally~~ when I applied -BE when calling variants with the bcftools, the missing locus could be detected again. Inspired by this post: http://seqanswers.com/forums/showthread.php?t=16786.

[wzhjlau2009]

i also meet the same problem! may i have a chat with you? hellohenry.my email:[email protected] QQ:872664567