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!
-
-
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
-
If you find any problem don't hesitate to contact us.Comment
-
Thanks a lot!Comment
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment