options

• Integrate --help
• Integrate mkbwt --help
• Integrate fusion -help

Integrate --help

INTEGRATE version 0.1c
          Discover fusions by combining RNA-Seq and WGS data sets*

usage:    Integrate <subcommand> [options] list of data sets

Integrate subcommands include:

          fusion:   call fusions.
          mkbwt:    build BWTs for reference genome. This has to be run one time before running subcommand fusion.

*Note:    Integrate can run with RNA only data sets.

Integrate mkbwt --help

INTEGRATE version 0.1c

Creat directory:

    mkdir directory_to_bwts

Run subcommand mkbwt:

    Integrate mkbwt (options) reference.fasta

    options:

            -mb  integer  :     sequences in the reference fasta that are shorter than this value        default: 10000000
                                are not included in the evaluation of repetitive reads.
            -dir string   :     directory to store the BWTs.                                             default: ./bwts

Integrate fusion -help

INTEGRATE version 0.1c

Make sure mkbwt has been run:

Integrate fusion (options) reference.fasta annotation.txt directory_to_bwt accepted_hits.bam unmapped.bam (dna.tumor.bam dna.normal.bam)

options: -cfn      integer : Cutoff of spanning RNA-Seq reads for fusions with non-canonical
                             exonic boundaries.                                                         default: 3
         -rt       float   : Normal dna / tumor dna ratio. If the ratio is less than
                             this value, then dna reads from the normal dna data set
                             supporting a fusion candidates are ignored.                                default: 0.0
         -minIntra integer : If only having RNA reads, a chimera with two adjacent
                             genes in order is annotated as intra_chromosomal rather than
                             read_through if the distance of the two genes is longer than
                             this value.                                                                default: 400000
         -minW     float   : Mininum weight for the encompassing rna reads on an edge.                  default: 2.0
         -mb       integer : See subcommand "mkbwt".
                             This value can be larger than used by mkbwt.                               default: 10000000
         -reads    string  : File to store all the reads.                                               default: reads.txt
         -sum      string  : File to store summary.                                                     default: summary.tsv
         -ex       string  : File to store exons for fusions with canonical exonic boundaries.          default: exons.tsv
         -bk       string  : File to store breakpoints                                                  default: breakpoints.tsv

This version of Integrate works in the following situations:
(1)having rna tumor, dna tumor, dna normal
(2)having rna tumor, dna tumor
(3)having rna tumor

Integrate will only use sequences in reference.fasta.
Chr names with and without "chr" are regarded as the same, e.g. chr1 = 1.
The rna and dna bams can be from alignments mapped to different reference files with different order of the sequences and their names with or without "chr". However, The versions should be the same, e.g. hg19. (Also, the same as in annotation.)
The tumor and normal dna bams should be mapped to the same reference file.

For rna tumor: accepted_hits.bam is a bam file containing mapped rna reads. unmapped.bam is a bam contains the not mapped rna reads. If they have been merged into one bam, just use merged.bam twice in the command line.

For dna bams: If solt-clips are provided, then Integrate is trying to search rearrangement breakpoints, otherwise, only paired reads may be included in the analysis.

If having rna normal only or having both rna and dna normal data sets. These data sets can be run to find non somatic events.
e.g. Integrate fusion -normal (options) reference.fasta annotation.txt directory_to_bwt accepted_hits.normal.bam unmapped.normal.bam (dna.normal.bam)