Most Popular and fancy SNP analysis tools Comparison: Plink, SNPassoc, SNPRelate

Question

[Shicheng Guo]

Hope to find some summary materials for the comparison among PLink, SNPRelate, SNPassoc et.al. Any suggestion? I will add more materials after I master these tools:

1, SNPRelate: Multiprocessing, Support more variation (SNP, CNV, SNV)

2, PLink: hard to do advance analysis

3, SNPassoc: support traditional association study

4, Gemma: Genome-wide efficient mixed-model association (GEMMA)

[Bioinformatics_NewComer]

Gemma might be added

[Shicheng Guo]

Nice Nature Genetics paper： Gemma: genome-wide efficient mixed-model association (GEMMA)

[Bioinformatics_NewComer]

I'm looking for a association package/suite that can help with disproportionate numbers of case-control. Something weighted. I'd data that with one-tenth number of cases of controls, results were of course messy. Any suggestions?

Answer 1

[Philipp Bayer]

Some more:

GAPIT: Nice R-package based on EMMA, does everything including the plotting in one box, a bit hard to customise intermediate steps, in my experience much more conservative than PLINK (i.e., fewer associated SNPs)

TASSEL: Easy to use, point-and-click interface, doesn't seem to support correcting for multiple testing? Lots of tutorials out there are for older versions, have to be careful. Can do MLM and GLM associations.

pySEER: Supports SNP, PAV, indel, and k-mer association, wonderful documentation: http://pyseer.readthedocs.io/en/master/

(Personally I believe k-mer based association studies will eat SNP based association studies soon, less bias from reference genomes)