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Changelog
Full Commit List : https://sourceforge.net/p/atlas2/code/commit_browser
Trunk
- VcfPrinter: New flag "--indel" added to handle indels when merging vcfs.
- VcfPrinter: Added unit test cases for VcfLine class.
Stable
Version 1.4.3 (03-01-2013)
Atlas-SNP2
- Add an option “-w” to only evaluate the sites in a given VIP list.
- Atlas-SNP2 will evaluate the VIP sites of extra-high coverage, regardless of the setting of “maximum coverage”. And these VIP sites will be marked as “high_coverage” in the filter column if they are higher than “maximum coverage”. (In previous version, these sites are skipped)
- Require the users to set the sequencing platform. The labels are “--Illumina”,”454_FLX”,”454_XLR”. To make it compatible to previous submission scripts of various users, “-s” for Illumina data will still work.
Atlas-INDEL2
- Bug fixed in -always-include option which caused included low-Quality sites to be printed with a QUAL of 'false' and missing the P value. See ticket.
- Removed the ReqIncl filter, this is now only indicated in the INFO column.
VcfPrinter
- New "--fast" implemented. Since it uses memory for storing variant information across all samples should only be used to merge small number of sites (~50000) across small number of samples (~20).
- New option "--cluster". Designed to be used in a HPC environment. Useful when merging millions of variants across thousands of samples.
- Logging implemented.
Version 1.4.1 (09-06-2012)
Atlas-SNP2
- Added always-include option
- Added show-filtered option
- Added version information and running commend in the VCF header
Atlas-Indel2
- Added alway-include option
- Added show-filtered option
- Fixed bug caused by passing a non-fasta reference genome
- Fixed bug occationally returning infinite P value in INFO column
- Fixed bug caused by reads mapping past the end of the reference genome
- Made Atlas2-Indel2 more tolerant of malformed SAM lines
- For Illumina/ 454 platforms
Version 1.3 (08-18-2011)
Atlas-SNP2
- Add a new option to call SNP on given regions or by chromosomes
- Change the default maximum coverage for SNP calling to 1024
- For pair-end data, add an option to use insertion size for mapping quality control
- Improve the performance of crossmatch2SAM
Version 1.2 (01-18-2011)
This is a major upgrade of Atlas2
Atlas-SNP2
New features
- one-stop running: take sorted BAM files and reference file as input and output SNP genotypes in VCF format
- use mapping quality score as alignment quality control
- use insertion size as mapping quality control for pair-end re-sequencing data
- more filters are integrated for higher quality SNP calls
Performance
- whole genome SNP calling is doable on a typical PC with 4G memory now. In our test, it can process 1 million reads per 5 minutes for whole exome SNP calling only using one CPU core of Xeon 5520 and 4G memory
Bugs fixed and compatibility
- more robust to alignment errors
- crossmatch2SAM tool is compatible to Ruby 1.9.X now
- a few minor bugs
Version 1.1 (04-26-2010)
Atlas-SNP2
- added a heuristics-based genotyping module
- added a column of “numRefReads_afterFilter” in Atlas-SNP2 result file
- revised the header line in Atlas-SNP2 output file to be more explicit
- skipped duplicate reads masked in the BAM files when processing
- added an option for the user to setup the max number of alignments allowed to be piled up at a particular site
- printed more running information and more detailed alignments statistics
- more robust to various alignments errors
- fixed several bugs
Version 1.0 (01-20-2010)
Atlas-SNP2
- added Illumina Platform support
- all calculations are now based on required fields of SAM to get maximum compatibility
- added CIGAR and reference sequence test code
- used pileup number to calculate TotalCoverage
- improved performance
- migrated to Ruby 1.9
- many minor improvements
Draft release version 0.1 (12-10-2009):
initial implementation
initial support of SAM files
For SOLiD platform (08-18-2011)
- Major SNP calling model update
- Support GATK base quality re-calibrated BAM by using OQ tags
- Call SNPs only on regions defined in a bed format file
- Output the SNP calls in vcf format directly
Atlas-Indel2
- updated SOLiD model and adjusted P cutoffs
- changed -P cutoff to apply to both 1bp insertions and deltions (rather than just 1bp deletions)
Version 0.3.1
Atlas-Indel2
- added options to use original base quality
- fixed bug that sometimes returned success exit code when there was a failure
- fixed bug in simple_genotyper that caused samples with exactly 0.05 variant read ratio to be 0/0
- fixed bug in simple genotyper that caused genotypes to occationaly read ./.
- fixed bug in bed_filter that was filtering some on-target reads in very small target regions
Version 0.3
Atlas-Indel2
- updated SOLiD and Illumina models and recalibrated default settings
- implemented the ability to input a bed file to call only on-target indels
- switched from using z cutoffs to using p cutoffs
- modified 1bp p cutoff to only filter 1bp deletions
- fixed bug where the strand direction filter failed to be enabled
- added check for proper ruby version
- fixed bug that occasionally allows an indel quality of 110 (max should be 100)
- minor code-structure changes
Version 0.2.1
Atlas-Indel2
- added read_level model and improved site level model for SOLiD data
- adjusted default SOLiD z cutoff to 0.0 (to reflect new model)
- added check for proper ruby version
- minor codes structure changes
- added additional heuristic filter that allows for a stricter z cutoff for 1bp indels, very useful for SOLiD data
- integrated heuristic genotyping –implemented
- fixed bug where Atlas-Indel2 crashes if a BAM chromosome is not in the reference
- now will keep ‘chr’ in the chromosome label if it is in the BAM
- the depreciated script "Atlas-Indel2-Illum-Exome.rb, has been removed. Please use Atlas-
Indel2.rb with the -I flag instead
Version 0.2
Atlas-Indel2
- Implemented regression model for SOLiD data. You must now specify a regression model with
-S or -I. - Renamed main script to Atlas-Indel.rb.
- Modified Reference sequence class to allow for unsorted reference genomes.
- Added the indel z to the info column of the VCF output (not included after running VCF printer).
- Now echos all settings back onto the command line.
- Fixed a bug that caused loss of precision in the normalized variant square variable of the
Illumina site model. - Fixed a bug in the depth coverage algorithm that caused reads not to be counted in total depth at the deleted sites.
- Fixed the sample columns order to be comaptible with vcfPrinter.
- Removed "x flagged lines skipped" message at end of run.