Fixed two things in the filter_hwe_by_pop.pl script that prevented compatibility with newer versions of vcftools (>0.1.11):
1) added extra variables to capture two extra p-values calculated by newer versions
2) recent versions of vcftools print to STDERR instead of STDOUT - this update uses shell redirection within the system calls to redirect the STDERR to STDOUT. This fixes the compatibility problem with newer versions and maintains backwards compatibility with older versions.
jpuritz
commented
7 years ago
Fixed two things in the filter_hwe_by_pop.pl script that prevented compatibility with newer versions of vcftools (>0.1.11):
1) added extra variables to capture two extra p-values calculated by newer versions 2) recent versions of vcftools print to STDERR instead of STDOUT - this update uses shell redirection within the system calls to redirect the STDERR to STDOUT. This fixes the compatibility problem with newer versions and maintains backwards compatibility with older versions.