Snv_call

Type motus snv_call to print the snv_call options.

OPTIONS:

• -d (DIR), Call metaSNV on all bam files in the directory. [Mandatory]
• -fb (DIR), Coverage breadth: minimal horizontal genome coverage percentage per sample per species. Default=80
• -fd (DIR), Coverage depth: minimal average vertical genome coverage per sample per species. Default=5
• -fm (DIR), Minimum number of samples per species. Default=2
• -fp (DIR), FILTERING STEP II: Required proportion of informative samples (coverage non-zero) per position. Default=0.9
• -fc (DIR), FILTERING STEP II: Minimum coverage per position per sample per species. Default=5
• -t (DIR), Number of threads. Default=1.
• -o (DIR), Output directory. Will fail if already exists. [Mandatory]
• -v (INT), verbose level: 1=error, 2=warning, 3=message, 4+=debugging. The default value is 3.
• -K, Save in the output directory all the files and directories produced by metaSNV. By default cov, distances, filtered, snpCaller are deleted

OUTPUT:

• coverage information for each mOTU, both horizontal (cov.tab file) and vertical (perc.tab file) (output directory)
• per mOTU filtered allele frequencies of identified SNVs across samples (filtered folder)
• per mOTU genetic distances between samples, both Manhattan (mann.dist files) and major allele (allele.dist files) (distance folder).