Entering edit mode
7.9 years ago
hrenchert747
▴
50
GATK throws errors on VCF file comparison (VCFs from the NextGene software output). Please advise a better solution for the comparison of 50-300 VCFs with an aim to find distinctive genes. Thanks.
which error ?
Could you please specify what you mean by find "distinctive" genes? And exactly what kind of comparisons are you trying to make?
Thx. Need to find unique genes between samples. NextGene can run only 6 projects to find differences among mutation profiles, GATK cannnot digest NG outputs correctly. Need the other tool, which I don`t know yet.
I am still not sure exactly what you mean, but it sounds like the software SKAT-O might help you. The problem with looking at differences between genes in a sample is that these variants are linked. SKAT-O has a statistical framework capable of weighting these only insofar as they are not linked to avoid "double-dipping" and also allows covariate control for your analysis. Finally it can work with rarer variants, which may be better for you since you have sequencing, not array, data. http://www.hsph.harvard.edu/xlin/pub/skat-o.pdf