EXAMPLES

Run pcr format SV calls:

tigra-sv washu_pilot2_trio_large_deletions.pcr pcr_filelist.txt

Run breakdancer format SV calls:

tigra-sv -b breakdancer.sv /gscuser/tumor.bam /gscuser/normal.bam

TIGRA-SV

NAME

TIGRA-SV - a tool that conducts targeted local assembly of structural variants (SV).

SYNOPSIS

tigra-sv sv_file a.bam b.bam …

tigra-sv sv_file bam_list_file

DESCRIPTION

TIGRA-SV is a program that conducts targeted local assembly of structural variants (SV) using the iterative graph routing assembly (TIGRA) algorithm (L. Chen, unpublished). It takes as input a list of putative SV calls and a set of bam files that contain reads mapped to a reference genome such as NCBI build36. For each SV call, it assembles the set of reads that were mapped or partially mapped to the region of interest (ROI) in the corresponding bam files. Instead of outputing a single consensus sequence, TIGRA-SV outputs all the alternative alleles in the ROI as long as they received sufficient sequence coverage (usually >= 2x). It is shown that TIGRA-SV is quite effective at improving the SV prediction accuracy in short reads analysis and can produce accurate breakpoint sequences that are valuable to understand the origin, mechanism and pathology underlying the SVs.

OPTIONS

-A INT

Esimated maximal insert size [500]

-l INT

Flanking size [500]

-w INT

Pad local reference by additional [200] bp on both ends

-q INT

Only assemble reads with mapping quality > [1]

-N INT

Number of mismatches required to be tagged as poorly mapped [5]

-p INT

Ignore cases that have average read depth greater than [1000]

-Q INT

Minimal BreakDancer score required for analysis [0]

-I STRING

Read intermediate files from DIR instead of creating them

-L STRING

Ignore calls supported by libraries that contains (comma separated) STRING

-c STRING

Specify chromosome for position 2 to parallelzing job

-b

Check when the format is in breakdancer

-r

Whether write reference to a file with .ref.fa as the suffix

-d

Whether to write dumped reads to a file with .fa as the suffix

-R

Reference file location with the full path

AUTHOR

Xian Fan, Ken Chen, Lei Chen

DISCLAIMER

This software is provided “as is” without warranty of any kind.