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Atlas 2

Release History


a) For Illumina/454 platforms

Version 1.4.1 (09-06-2012)

  • Added always-include option

  • Added show-filtered option

  • Added version information and running commen in the VCF filter

Version 1.3 (08-18-2011)

  • 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 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


  • 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)

  • 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)

  • 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

b) For SOLiD platform

Version 1.0 (08-18-2011)

  • Major SNP calling model update

  • Support GATK base quality re-calibrated BAM by using OQ tags

  • Call SNPs only on regions define in a bed format file

  • Output the SNP calls in vcf format directly

Draft release version 0.1 (01-26-2011)

  • Initial implementation

Previous release: Atlas-Indel2

Version 1.4.1

  • Added always-include option

  • Added show-filtered option

  • Fixed bug caused by passing a non-fasta reference genome

  • Fixed bug occasionally 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

Version 1.0

  • Updated SOLiD model and adjusted P cutoffs

  • Changed -P cutoff to apply to both 1bp insertions and deletions (rather than just 1bp deletions)

Version 0.3.1

  • 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 occasionaly read ./.

  • Fixed bug in bed_filter that was filtering some on-target reads in very small target regions

Version 0.3

  • Updated SOLiD and Illumina models and recallibrated 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

  • 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 (02-09-2011)

  • Version 0.2 software

  • Version 0.2 documentation

  • Implemented regression model for SIOiD data. You must now specify a regression model -S or -l.

  • 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 compatible with vcfPrinter. Removed "x flagged lines skipped" message at end of run.

Version 0.1 (12-2011)

Previous release: Atlas-SNP2:

Version 1.1 (04-26-2010)

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Version 1.0 (01-20-2010):

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Version 0.1 (12-10-2009):


Solid-genotyper is a SNP discovery and genotyping tool for high coverage SOLiD data. This tool combines a logistics regression model and heuristics methods to characterize systematic sequencing error and overcome mapping bias issue.

Draft release version 0.1 (01-26-2011):

Draft release version 0.1 (01-26-2011):

  • Initial implementation

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