Hi, Ashwani The next step is GL. Please check the wiki: https://sourceforge.net/p/snptools/wiki/Best%20practices%20of%20integrated%20SNP%20analysis/...
Ashwani, "chr" is actually "$chr", it is 19 in your case.
Ashwani, does the ebd files have the right path?
Best practices with SNPTools
tweak makefile to make it compatible to latest gcc