Variant Detection Software Review
Just trying to get a feel for the pros and cons of all the variant detection algorithms that are out there before I choose one algorithm.
I haven't seen any comparative analyses done like I have for assemblers and mappers and I think it would be beneficial. I've only used samtools and a little bit of gatk and freebase since those are the popular ones, but would like to know how the others perform. Also, I haven't seen many that are able to handle non-diploid organisms which is important to know.
The how-to SNP detection did well to suggest some software packages that can do this (http://seqanswers.com/wiki/How-to/SNP_detection) and also cited a couple papers that did some comparative analysis with only a few of the algorithms mentioned on that same page. However, a text search for 'varia' on the software list showed 100 hits (http://seqanswers.com/wiki/Software/list).
Work flows, workarounds, cautions are all appreciated.
I haven't seen any comparative analyses done like I have for assemblers and mappers and I think it would be beneficial. I've only used samtools and a little bit of gatk and freebase since those are the popular ones, but would like to know how the others perform. Also, I haven't seen many that are able to handle non-diploid organisms which is important to know.
The how-to SNP detection did well to suggest some software packages that can do this (http://seqanswers.com/wiki/How-to/SNP_detection) and also cited a couple papers that did some comparative analysis with only a few of the algorithms mentioned on that same page. However, a text search for 'varia' on the software list showed 100 hits (http://seqanswers.com/wiki/Software/list).
Work flows, workarounds, cautions are all appreciated.