SVTools

Tools for processing and analyzing structural variants.

Table of contents

• bedpeToVcf
• vcfToBedpe
• lumpyToBedpe

bedpeToVcf

Convert a LUMPY BEDPE file to VCF

Usage

usage: bedpeToVcf [-h] [-t TOOL] -c SAMPLE_CONFIG [-f FASTA] [-b BEDPE]
                  [-o OUTPUT]

options:
  -h, --help            show this help message and exit
  -t TOOL, --tool TOOL  Tool used to generate calls
  -c SAMPLE_CONFIG, --sample_config SAMPLE_CONFIG
                        Tab delimited sample config file of NAME id TYPE
                        (Example: NA12878 10  PE)
  -f FASTA, --fasta FASTA
                        Indexed fasta file of the reference genome
                          (pysam required if using this option)
  -b BEDPE, --bedpe BEDPE
                        BEDPE input (default: stdin)
  -o OUTPUT, --output OUTPUT
                        Output VCF to write (default: stdout)

Example

bedpeToVcf -b samples.sv.bedpe -c samples.config > samples.sv.vcf

Example sample config file (tab delimited)

NA12877	10	PE
NA12877	11	SR
NA12877	12	RD
NA12878	20	PE
NA12878	21	SR
NA12878	22	RD
NA12879	30	PE
NA12879	31	SR
NA12879	32	RD
NA12880	40	PE
NA12880	41	SR
NA12880	42	RD

vcfToBedpe

Convert a VCF file to a BEDPE file

Usage

usage: vcfToBedpe [-h] [-v VCF] [-o OUTPUT]

optional arguments:
  -h, --help            show this help message and exit
  -v VCF, --vcf VCF     VCF input (default: stdin)
  -o OUTPUT, --output OUTPUT
                        Output BEDPE to write (default: stdout)

Example

vcfToBedpe -v samples.sv.vcf > samples.sv.bedpe

lumpyToBedpe

Convert a LUMPY BEDPE file to an extended BEDPE for easier filtering

Usage

usage: lumpyToBedpe [options]

options:
  -h, --help            show this help message and exit
  -b BEDPE_FILE, --bedpe_file=BEDPE_FILE
                        BEDPE file
  -c CONFIG_FILE, --config_file=CONFIG_FILE
                        Tab-delim sample config file of NAME id TYPE.
                        Example:NA12878 10  PE

Output format

Tab delimited

1: chromosome a;
2: coordinate start a (leftmost position of the first breakpoint-containing genomic interval)
3: coordinate end a (rightmost position of the first breakpoint-containing genomic interval)
4: chromosome b;
5: coordinate start b (leftmost position of the second breakpoint-containing genomic interval)
6: coordinate end b (rightmost position of the second breakpoint-containing genomic interval)
7: breakpoint ID;
8: support (total number of read-pair + split-read measurements)
9: strand a (direction of breakpoint relative to read mappings; "+" indicates to right, "-" to left)
10: strand b (direction of breakpoint relative to read mappings; "+" indicates to right, "-" to left)
11: variant type (DEL=deletion; DUP=duplication; INV=inversion; INT=inter-chromosomal)
12: evidence types detected (PE/SR)
13: strand combinations clustered (useful for inversions and reciprocal translocations)
14: sampleList (list of samples that have the breakpoint)
15: evidenceSampleList (detailed list of samples, evidence types, and evidence observations)
16-N: sample_N total support

Example

lumpyToBedpe -b NA12878_S1.sv.bedpe -c NA12878_S1.sample.config > NA12878_S1.sv.ext.bedpe

Example sample config file (tab delimited)

NA12877	10	PE
NA12877	11	SR
NA12877	12	RD
NA12878	20	PE
NA12878	21	SR
NA12878	22	RD
NA12879	30	PE
NA12879	31	SR
NA12879	32	RD
NA12880	40	PE
NA12880	41	SR
NA12880	42	RD