run-mpileup: run bcftools stats with "-c both" by default
run-shapeit: recognise "." regions; Use the newest version of shapeit by default
run-impute2: chunk-specific options moved up in the sample config to be less likely overlooked
vcf-impute2: Pad missing GLs at multiallelic sites
run-shapeit: Use chunk_by_ref only when also ref_vcf is given
run-impute2: Use chunk_by_ref only when also ref_vcf is given
RunnerLSF: Fix in bswitching, seconds instead of minutes were used