I am analyzing some whole genome data and at the moment I use GATK for indels and SNPs. What are some other tools or pipelines out there for whole genome analysis?
For example I read the HugeSeq paper, and I saw pindel, CNVnator, BreakDancer, and BreakSeq. Does anyone have other recommendations or preferences among these ?
And do you (or how do you ) combine results from two programs, such as UnifiedGenotyper and Pindel?
For example I read the HugeSeq paper, and I saw pindel, CNVnator, BreakDancer, and BreakSeq. Does anyone have other recommendations or preferences among these ?
And do you (or how do you ) combine results from two programs, such as UnifiedGenotyper and Pindel?
Comment