Welcome to the MELT homepage.

- Made substantial runtime improvements to IndivAnalysis. These improvements require that you have run samtools fixmate or similar algorithm to add MC and MQ tags to your cram/bam file. Please see the documentation for more details (Section 7.1 - Preprocessing .bam Files for MELT & 6. MELT Options). Two major notes with this release: 1.) Files without MC and MQ tags can still be used with MELT, albeit with longer runtimes; 2.) Information reported by MELT may be very slightly different than previous versions. This should be limited to +/- 1 variant site per genome and +/- 1 to the LP/RP INFO tags.
- Genotype remains relatively slow when using MELT on CRAM files. We are still searching for improvements to our methodology.
- Various code readibility improvements.

- Updated the version of htsjdk that MELT uses to version 2.22.0. This results in internal changes to how code is implemented and should not effect MELT output.

- First new public release in over a year - the 2.2.0 release incorporates all changes from 2.1.5 to now.
- MELT no longer writes a chromosome mask file in ./MELTWorkingDir/tmp/ directory. It is now stored in memory.
- Internal changes to code for Alignment to MEI references. Functionality is same as previous versions.
- Fixed a bug related to where, on rare occasions, MELT would fail during GroupAnalysis due to not being able to find discordant pairs at an identified locus.
- Added a new error message that actually makes sense for when MELT cannot find an index for a BAM/CRAM file.

- Internal changes to how MELT handles the transposon reference mask.

- Small optimization for CRAM use.
- Added DP and AD tags to the MELT VCF file. These report the number of reads that MELT assessed and number of these reads that supported the insert site, respectively.
- Set the -c options to “not required”. MELT will now calculate coverage on it's own from the first chromosome in the .fai index starting at the value of -d (so default position 1,000,000). This calculated value can be overriden by either setting -c or putting a second column in the bamlist file as before.

- Fixed a bug where the -exome flag was not working with MELT Single (thanks to verne91 for reporting).
- Implemented htsjdk version (2.16.0)
- MELT now supports CRAM.
- Please note, to use CRAM format files you will need a working 'samtools' binary either in your path or supplied via the -samtools option.
- MELT has been tested with the latest changes to ensure results are identical for BAM files between MELT versions. This has not been completely verified for CRAM format files.
- Various under the hood movement in the MELT source code to make it easier to maintain.

- Changed slightly how gene reporting works within MELT. Will now report ALL overlaps with file provided by -n seperated by |.
- Several small bug fixes.

- Fixed bug in MELT-Deletion that caused issues when the reference genome was being masked (Thanks M. Okhovat for bug report).
- Added the '-sr' flag for filtering reads without SR support during the GroupAnalysis step.
- Added SR flag to the MELT MEI VCF output which displays the total number of SRs per site.

- Fixed a bug in the genotyping step that caused organisms with small chromosomes/contigs to fail at the genotyping step (Thanks to M. Volpe for reporting).

- Implemented new htsjdk version (2.11.0).
- To keep MELT current with relevant libraries in preperation for additional available datasets.
- Bug Fixes:
- Removed old code supporting multi-threaded discovery.
- Fixed an issue where MELT would fail if the BAM file header from the source BAM was too large (Thanks M. Volpe for reporting).
- Fixed an issue where sites would fail on estimating the breakpoint due to lack of high quality reads (Thanks to R. Collins for reporting).
- Fixed an issue where MEIs being discovered at coordinate “0” on any given contig where resulting in a genotype failure (Thanks to M. Volpe for reporting).

- First post-publication update to MELT.
- Fixed a bug in MELT-DEL which would cause MELT to freeze when dealing with sites immediately adjacent to ’N’ sequence in reference genomes (Thanks J. Korstian for original bug report).
- Fixed a bug in MELT-DEL where ‘./.’ genotypes would be reported if no ‘MD’ tag was present to determine mismatches.
- Fixed a bug where excessive supplementary alignments were causing MELT to have excessive runtimes during the IndivAnalysis step.
- Added a new flag when running MELT with exome data: -exome
- This flag changes the minimum amount of evidence necessary to place a site in the putative hits list during IndivAnalysis
- Changed how MELT handles tmp directories to avoid confusing errors when running a large number of files at the same time through MELT-Split.
- Changed number of records merged into the final VCF file from 5,000 to 1,000 to better accommodate large datasets.
- Added the “ac0” FILTER for sites that did not genotype in the final VCF merge.
- MELT no longer filters AF = 0 sites when making the final VCF.
- This can be disabled with the 'ac' flag.
- Improved scalability of the MELT genotyper when assessing excessively high coverage genomes (e.g. > 60x) to remove false positive sites.
- Added a filter (lc) in the final MELT vcf for MEIs abutting low complexity regions.
- This does not filter sites automatically, but flags them as lower confidence sites.
- Functions by scanning ±25bp from the breakpoint and looking for runs of 15 or more bases of A,T,C,G or any combination of the two (i.e. an AT micro satellite).
- WARNING: This filter has not been testing using Whole Genome data yet (only exome) and may lead to lower sensitivity in relevant datasets.

- Implemented a new Genotyping optimization for short elements (i.e. SINEs) that improves het -> hom genotypes.
- Internal changes in how MELT handles options.
- MELT now has a single set of options that are used by all MELT pipelines.
- Excludes CAlu, LINEU, and BuildTransposonZIP.
- Internal changes on how MELT performs analysis in MELT-SGE and MELT-Single modes.
- Fixed a bug that caused the wrong max-coverage filter to be used in MELT-Split mode.
- Fixed a bug that was incorrectly handling the ‘-a’ flag (BWA-aln was used for alignment).
- Changed the transduction module to three parts.
- Use ‘Source’ to generate a list of source L1s for transduction analysis.
- Can now preprocess bam files for transductions. This should hopefully increase the speed of transduction finding.
- Now use TransductionMerge of a list of bam files to finalize VCF annotation.
- Changed the output in the MELT VCF INFO field for transductions.
- MESOURCE now has the format <SOURCE CHR>,<SOURCE POS>,<SOURCE TYPE [REF || nonREF]>,<GENOTYPE CONCORDANCE>,<TOTAL SUPPORTING READS>,<TRANSDUCTION SIZE>
- Additional INFO field METRANS has the info <CHR>,<TRANSDUCTION SOURCE START>,<TRANSDUCTION SOURCE STOP>,<TRANSDUCTION STRAND>.
- See MELT manual for more details.
- Fixed a bug where MELT would report a 5’ Inversion event rather than reporting no measurement (-1).

- Slight efficiency improvements in step 1 of the MELT-Split pipeline.

- Added better description/explanation for the error reported in GroupAnalysis when MELT doesn’t find any hits in the IndivAnalysis step.
- Added check to the MakeVCF step to ensure all genotyping finished properly.
- Fixed error in MELT transduction finder due to unrecognized bam names.
- Fixed an error in MELT genotype where MEI masking was not working properly.

- Added a format check for the genome annotation file (provided with -n).
- Updated some language in the help dialog provided by --help/-h.
- Several small bug fixes.
- Fixed an error in the manual that pointed to the wrong human reference file to download in the 'MELT Quick-Start Guide' section

- Initial Release
- Several improvements beyond MELT v1.0 used for the 2015 Nature publication, see our paper for more details.