Index

A

Annovar Annovar databases Installation Annovar databases Annovar Installation Arguments --CNV --Fusion --Verbose, [1] --cl --cu --fvaf --gene --keep, [1] --name --output --popfreq --quiet --rave --reads --source

D

Deamination Score

G

GRCh37

H

hg19	human reference

I

Installation Annovar Annovar databases Extra modules Requirements Scripting Languages Testing

Ion Torrent CNV Processing

L

Logging

M

MOI Counts Table MOIs MOMA Basic Usage CNV output Data sources Filtering Arguments Fusion output Inputs Logging Optional Arguments Output Package structure Resource files Setup Technical Details, [1] Troubleshooting Tutorial Workflow diagram output files

Mutations of Interest

O

Output CNVs Fusions SBS-6 small variants; SNVs / Indels

S

SBS-6

Single base substitution matrix small variants

T

Technical Details, [1] Troubleshooting Missing variants Other strategies Pipeline errors

Ts/Tv TSO500 Torrent CNV Processing

V

Variant Counts Table Variant Types CNV Fusion SNV/Indel small variants

Variants of Unknown Significance VuSes