SNVer

In this version, SNVer supports VCF 4.1 instead of VCF 4.0. Thanks to Yunfei Guo for the suggestions.

Fix a small bug for outputting INDELs of SNVerPool in SNVer-0.5.1. Thanks to Bo Zhu for the testing.

This version of SNVer has been recompiled using Java 1.6. The previous version was compiled by Java 1.7. It may produce java.lang.UnsupportedClassVersionError, due to a higher JDK during compile time and lower JDK during runtime. Thanks to Jharna Miya for reporting this issue.

The new version includes a few bug fixes:
1. Minus one of all the indel positions to make SNVer consistent with other software. Thanks to Bo Zhu for pointing this out.
2. Fix a bug when the reads go beyond the reference boundary.
3. Fix a bug for computing total depth, which may affect other calculations, e.g alternative allele frequency. Thanks to David Ries and James Kijas.
4. Add a post-processing step to fix genotype as heterozygous in case of low frequency variants. Thanks to Yoojin Hong for the sugguestion.
5. Fix a bug of making incorrect variant call when the reference is lowercase. Thanks to Lucy Stead for the discussion.

SNVerGUI paper, "SNVerGUI: A desktop tool for variant analysis of next generation sequencing data", has been accepted by Journal of Medical Genetics.

Fix a bug when computing DP for INDEL, which leads to incorrect PV and GT if DP is smaller than AC. SNVerGUI is updated with SNVer-0.4.1.

SNVer now supports INDEL calling. The procedure and output files are similar to SNV detection. indel.raw.vcf and indel.filter.vcf will be the output files.

1. Fix a bug when computing AF in SNVerPool, NP now is the number of non-NA pools.
2. Reformat the output printed in the console.

SNVerGUI-1.0, a desktop tool for variant detection from next generation sequencing data, is released. We thank Riena Project for providing the RCP platform with such excellent user interface components. The software for different platforms are now available at SNVerGUI.

This version includes several improvements:
1. Support query for snp_id, if users provide a dbSNP file and the column number of chr, pos, snp_id.
2. Add "PASS" and "FAILED" in FILTER column in VCF.
3. Set the allele frequency threshold(-t) to be 0 as default for SNVerPool.

The new version includes several improvements and bug fixes:
1. Output INDEL count to fail.log when, at one particular site, SNVer observes the count of INDEL is greater than the alternative count of SNP. This change would temporarily print potential INDEL sites which user may be interested in.
2. Fix a bug of inaccurately computing the alternative count when adjacent to INDEL sites. Thanks to Alan Bergland for pointing this out and making an example to reproduce the error.
3. Print the running progress on console.
4. Add a header for fail.log.
5. Fix a bug of wrong cutoff when the total line of raw.vcf is smaller than the comments of an empty VCF.

Three features for SNVer project have been added, including:
1. Javadoc is now available at Javadoc.
2. The source code is released at SVN Browse.
You can check out the latest source code with:
svn co https://snver.svn.sourceforge.net/svnroot/snver/trunk
3. Three mailing lists have been updated at Mailing Lists.

This release fixes several bugs and changes jar file structure to reduce the file size.
1. Fix a bug when picard returns that the reference index is -1.
2. Remove -b option in SNVerPool, which actually is no need in pooled sequencing data.
3. Enhance the configuration file in SNVerPool(-c option), which is now supporting different base quality and mapping quality thresholds among different pools.
4. Fix a bug when the posterior probability is Inf.
5. Change the default pvalue cutoff parameter to be "-p bonferroni=0.05".

This version includes 3 major improvements and several bug fixes:
1. SNVer is able to take SAM/BAM files as input and do the pileup by its own, the SAM/BAM manipulation is based on PICARD and SAM-JDK.
2. Address the memory issue in SNVerPool, which is now able to analyze whole genome pool sequencing data.
3. Instead of -e 0.01 error rate threshold in the previous version, the current version estimates the empirical error rate. See manual for more details.
4. Integrate FWER=0.05(default) in -p parameter, the output results are separated into two vcf files, one is called input.raw.vcf and the other is called input.filter.vcf according to the p-value cutoff uses.
5. Add two parameters for removing potential false positives, which are i) -a refers to at least how many supporting reads for alternative in each strand(default is 1); ii) -b refers to the allele imbalance issue, requiring the ratio of alt/ref would be greater than the threshold(default is 0.25).
6. Add -c for SNVerPool for loading different pool information, currently supporting different pool size(pools with different individuals). See manual for more details.
7. Fix a bug when computing the binomial test pvalue.
8. Add -u to inactivate strand bias test and fisher's exaxt test above this threshold(default is 30).

This release fixes two minor bugs.
1. Fix a bug in SNVerPool when parsing pileup files.
2. Fix a bug for posterior probability of GT=1/1 in the output.

This release includes the following bug fixes and changes.
1. The prior when calculating the posterior probability of 1/1,1/0,0/0 has been changed for analyzing individual data, -h option has been added to SNVerIndividual, where default is 0.001 for heterozygosity. See Manual for more detail.
2. Set default base quality threshold to 20.
3. Fix the bug of GT value=0/0 in the output SNV call set due to allele imbalance issue.

The first public release of SNVer is avaliable for download. SNVer is a statistical tool in analysis of both pool and individual NGS data. In the current release, SNVer takes SAMtools pileup files as input. SNVer will be able to extend to integrate the pileup function in later release.