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. |
|