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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!
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appreciaton
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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.Comment
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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....Originally posted by dpryan View PostComment
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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.Comment
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i also meet the same problem! may i have a chat with you? hellohenry.my email:[email protected] QQ:872664567Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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