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Hi, Can anyone suggest on tools/packages to detect SNPs? I have Illumina data and used bowtie for the alignment. For each detected SNP I would like to have the following fields for homozygous and heterozygous SNPs: actual number of reads for each base in my sample, the reference base and whether such a SNP exists in dbSNP and HapMap. Thank you!
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There's a lot of software to do that kind of analysis. We have develop a pipeline that covers most of your needs. You can take a look at:
We do not work in human, so we haven't added the HapMap part. -
Thanks! I will try it.Comment
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If you find any problem don't hesitate to contact us.Comment
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Thanks a lot!Comment
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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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