jpayne@0: jpayne@0: from multiple samples jpayne@0: jpayne@0: bowtie2 jpayne@0: samtools jpayne@0: snp-pipeline jpayne@7: python jpayne@0: jpayne@0: ./file jpayne@0: && cfsan_snp_pipeline merge_sites -v 4 -n "var.fit.vcf" ./file ./filtered_snps -o $snplist 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: http://snp-pipeline.readthedocs.io/en/latest/index.html jpayne@0: ]]> jpayne@0: jpayne@0: 10.7717/peerj-cs.20 jpayne@0: jpayne@0: