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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