Spanner is a c++ program for the detection of Structural Variation events from whole genome sequenced read pair data. It uses aligned read information in bam format and was developed in conjunction with the Mosaik alignment program

/usr/local/spanner/src

module load spanner

Sample session:

helix% module load spanner

helix% spanner -Z 1 -M mask.file -t

https://github.com/chipstewart/Spanner

USAGE: 

   spanner  [-Z ] [-S ] [-M ] [-w ] [-Q ]
            [-d ] [-t] [-a ] [-b] [-s] [-u ] [-c
            ] [-i ] [-x ] [-f ] [-p ]
            [-o ] [-R ] [--] [--version] [-h]


Where: 

   -Z ,  --Zmode 
     bam access mode (1=ZAtag, 2=SortedByReadName) 

   -S ,  --specialtag 
     prefix of element names in special reference

   -M ,  --MASKFILE 
     Event masking file

   -w ,  --fragtailwindow 
     p-value for frag window cut

   -Q ,  --qmin 
     minimum mapping q value

   -d ,  --debug 
     debug: interval>0, RD<0

   -t,  --text
     ascii text output

   -a ,  --anchorfile 
     name of anchor info file

   -b,  --build
     build span files

   -s,  --scan
     scan fragment length only

   -u ,  --uniquify 
     duplicate fragment removal

   -c ,  --contigs 
     regexp for allowed contigs

   -i ,  --infile 
     specify pre-built input files

   -x ,  --maxfrag 
     maximum number of fragments

   -f ,  --fragHist 
     name of fragment length histogram file

   -p ,  --prefix 
     output prefix

   -o ,  --outdir 
     name of SV output area

   -R ,  --rcp 
     name of parameter file

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.