Name | Modified | Size | Downloads / Week |
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README.txt | 2013-01-23 | 3.3 kB | |
SVDetect_r0.8b.tar.gz | 2013-01-23 | 618.4 kB | |
SVDetect_r0.8.tar.gz | 2011-12-05 | 616.5 kB | |
Totals: 3 Items | 1.2 MB | 0 |
==== SVDetect release notes ===== * r0.8b - 2013-01-22 New version of the "BAM_preprocessingPairs.pl" script (0.5) - update regarding the flag bitwise of the "one unmapped read" pairs with the SAM 1.4 specification format * r0.8 - 2011-12-06 - Parallelized computing in linking, filtering and cnv functions per chromosome - New perl libraries required : FileHandle - Parallel::ForkManager - Addition of the "num_threads", "tmp_dir", "split_mate_file", "split_link_file" parameters - Modified configurations files in the test sample Neuroblastoma * r0.7m - 2011-07-12 - Change of the parameters location in the config file: read1_length, read2_length, mates_file, cmap_file located in the <general> block - The <compare> block is now completely independent - Addition of the list_read_lengths parameter in the compare block (in case of different libraries) - Modified configurations files in the test sample - Identification of medium-size duplications for Illumina paired-end/mate-pair data * r0.7f - 2011-01-10 - The "File::Sort" perl library is not required anymore - The strand filtering decision has changed, links having two populations of different pair orientations are not discarded but splitted - The consistency of the sens strand orientation of pairs in the order filtering is now assessed for SOLiD mate-pairs - Identification of additional SV types according the balanced signatures of consistent mapped pairs - Identification of singletons (Illumina mate-pairs only), addition of the "singleton_sigma_threshold" parameter - Clusters with an undefined SV type are not discarded (type is "undefined") - Addition of the "final_score_threshold" parameter (post-filtering process) - The "links2compare" function requires BEDTools, addition of "min_overlap" and "same_sv_type" parameters - Modified configurations files in the test sample - New version of the "BAM_preprocessingPairs.pl" script (v0.4), lower and upper limits of ISIZE can be set for a better calculation of mu and sigma lengths - README update (v1.10) * r0.6d - 2010-09-10 -Sorting and removing fully overlapped links at the end of any filtering step -Faster compare algorithm -Few bug fixes * r0.6c - 2010-08-03 Bug fix in the tabulated file format for *.links.filtered files New version of the "BAM_preprocessingPairs.pl" script (0.3) - Bug fixes in the sam file name extension for BAM conversion - Easy input parameters : Illumina/SOLiD and paired-end/mate-pair boolean values * r0.6b - 2010-07-26 Addition of the perl script "BAM_preprocessingPairs.pl" located in the new scripts/ directory. * r0.6a - 2010-07-21 Addition of new features: - Use of different read lengths between ends in a pair (compatibility with SOLiDv4 paired-ends, ex. F3:50bp F5:35bp) - Output directory option - BAM file accepted as input format (SAMtools required) - Faster strand filtering process - Lower memory usage (>3X) - Score of the insert size filtering provided - Start coordinates in link files correspond to sequencing starts (=first base of reads instead of the leftmost position) - Best definition of breakpoint starts and ends for SOLiD data Removed features: - No filtered mate files created (links only) * r0.5 - 2010-04-30 First official release of SVDetect