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Latest version: https://github.com/bioinform/breakseq2/archive/2.2.tar.gz
For other versions, see "releases". https://github.com/bioinform/breakseq2/releases
The following Python packages must be installed:
BreakSeq2 is a python package and can be installed using
pip. To install type
pip install https://github.com/bioinform/breakseq2/archive/2.2.tar.gz. The current version
of BreakSeq2 is 2.2. In general, the install source would be https://github.com/bioinform/breakseq2/archive/version.tar.gz
The following is the list of required options for BreakSeq2
--samtools path: Path to samtools executable.
--bwa path: Path to BWA executable.
--bams bam1 bam2 ...: BAMs containing read alignments.
--reference path: Reference genome in FASTA format.
Below are some examples of running BreakSeq2
run_breakseq2.py --reference b37.fasta --bams bwamem.bam --work work --bwa bwa-0.7.12/bwa --samtools samtools-0.1.19/samtools --bplib_gff bplib.gff --nthreads 4 --sample NA12878
Note that the sample name is not a required option. If it is missing, then the unique sample name is inferred from the BAMs. If there is no unique sample name and none is specified on the command-line, BreakSeq2 will fail. In the above example, since the breakpoint library was specified as a GFF, the insertion sequence file bplib.ins must also be present. BreakSeq2 will use the directory
work for all the intermediate as well as the final output. Internally, BreakSeq2 uses the breakpoint
library in FASTA format, so the conversion from GFF to FASTA is done before the actual processing. BreakSeq2 uses parallelism whenever possible for best performance-in this case, 4 threads will be used for some steps of the processing.
run_breakseq2.py --reference b37.fasta --bams bwamem.bam --work work --bwa bwa-0.7.12/bwa --samtools samtools-0.1.19/samtools --bplib bplib.fa --nthreads 4
Note that since the breakpoint library was specified as a FASTA file, bplib.ins is not required here since the insertion sequences are already accounted for in the FASTA.
In general, type
run_breakseq2.py -h for a list of all command-line options.