jpayne@0: jpayne@0: and associated distance metrics jpayne@0: jpayne@14: bcftools jpayne@12: bzip2 jpayne@0: snp-pipeline jpayne@36: tabix jpayne@37: jpayne@0: jpayne@0: ./file && jpayne@0: cat ./file && jpayne@0: cfsan_snp_pipeline snp_matrix -o $snpma ./file && jpayne@0: cfsan_snp_pipeline distance -p $pairws -m $distma $snpma && jpayne@0: cfsan_snp_pipeline snp_reference -l $snplist -o $referenceSNP $reference jpayne@0: ]]> jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@38: jpayne@38: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: http://snp-pipeline.readthedocs.io/en/latest/index.html jpayne@0: ]]> jpayne@0: jpayne@0: 10.7717/peerj-cs.20 jpayne@0: jpayne@0: