How do I run BreakPointer?
Currently BreakPointer runs on Unix based machines. Requires BWA, Samtools and Matlab or MCR installed.
Usage
BreakPointer.sh matlab_dir sample_name rearrangement_predictions bam_file lane_black_list refdir insertionsize confidence_thres low_confidence_sidewithread low_confidence_sidewithread high_confidence_sidewithread high_confidence_sidewithoutread max_mismatches tipsize min_mismatches_in_tip max_N expand_pairs_extraction max_reads_fished readlen align_enough_reads split_penalty min_qual libdir first_rearrangement last_rearrangement
Some of the key parameters to the algorithm are described in detail in our publication.
| Argument | Description | Suggested Value |
|---|---|---|
| matlab_dir | The directory where Matlab or MCR is installed. | |
| sample_name | The name of the sample, used for setting the output file names. | Can be any string valid for a file name |
| rearrangement_predictions | Input text file with the predicted rearrangements estimation (by PEM). It is a tab delimited text file with a header row, containing 'chr1', 'chr2', 'pos1', 'pos2', 'str1','str2' columns which represent the predicated rearrangement (chromosome, position, and strand for the two breakpoints) a ‘tumreads’ column which represent how many discordant read pairs support the prediction, and a 'normreads' column representing how many discordant read pairs would be detected in a normal sample without the rearrangement, as a control. | |
| bam_file | Is the BAM file of the sample. The folder containing it should also contain an index. | |
| lane_black_list | Is a text file listing lanes that you wish to omit. If you don't have any you can specify "none" (suggested). | none |
| refdir | Is a directory containing the genome by text files named chr1.txt, chr2.txt, chr3.txt, ......, chrX.txt with the content of each chromosome as one single line. | |
| insertionsize | Average insertion size, or a range of likely insertion sizes (in bp). | 400 |
| confidence_thres | The number of supporting discordant pairs reads above which the highconfidence parameters (below) are used. | 6 |
| low_confidence_sidewithread | The estimated error in the loci prediction before the breakpoint, that is the side the supporting reads are on, when number of supporting discordant pairs is low. | 80 |
| low_confidence_sidewithoutread | The estimated error in the loci prediction after the breakpoint, when number of supporting discordant pairs is low. | 200 |
|
high_confidence_sidewithread |
The estimated error in the loci prediction before the breakpoint, that is the side the supporting reads are on, when number of supporting discordant pairs is high. | 40 |
| high_confidence_sidewithoutread | The estimated error in the loci prediction after the breakpoint, when number of supporting discordant pairs is high. | 50 |
| max_mismatches | The maximal percentage of mismatches allowed for a read to be considered partly aligned (and hence possibly spanning the breakpoint). | 30 (for MAQ), 80 (for BWA) |
| tipsize | The size (in bp) of the tip of the read to check partial alignment. | 7 (for MAQ), 15 (for BWA) |
| min_mismatches_in_tip | The minimal number of mismatches required in a tip so it will be considered a mismatched tip, and hence the read is a candidate for partly aligned read (and hence possibly spanning the breakpoint). | 2 (for MAQ), 5 (for BWA) |
| max_N | The maximal number of N allowed in a read for it to be considered partly aligned (and hence possibly spanning the breakpoint). | 10 |
| expand_pairs_extraction | Window size around predicted breakpoint to look for split reads. | 500 |
| max_reads_fished | Maximal number of reads to pull when looking for split reads. | 100000 |
| readlen | The read length (in bp). | |
| align_enough_reads | BreakPointer quits aligning after this number of split reads that support on the same breakpoint are found. | 20 |
| split_penalty | The penalty to BreakPointer score for splitting a read. | 8 |
| min_qual | The minimal score a split read needs to be considered (normalized by read length). | 0.75 |
| libdir | The path to a directory with GrabSplitReads.jar, align_each_bkpt5.bin, and links to BWA and Samtools. | |
| first_rearrangement | The first prediction to pinpoint. | 1 |
| last_rearrangement | The last prediction to pinpoint. |