Tools for processing and analyzing structural variants.
Convert a LUMPY BEDPE file to VCF
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)
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
Convert a VCF file to a BEDPE file
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)
vcfToBedpe -v samples.sv.vcf > samples.sv.bedpe
Convert a LUMPY BEDPE file to an extended BEDPE for easier filtering
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
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
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