Manual for vcftools: http://vcftools.sourceforge.net/man_latest.html
Explanation of sam flags: http://broadinstitute.github.io/picard/explain-flags.html
Zaugg Lab
USING PERSONALISED GENOMICS TO STUDY THE GENETIC BASIS OF COMPLEX DISEASES
Manual for vcftools: http://vcftools.sourceforge.net/man_latest.html
Explanation of sam flags: http://broadinstitute.github.io/picard/explain-flags.html