Performance and features - 18.11.2017
This release increases the speed of variant calling and improves the meta-alignment tool.
Meta-alignment - 19.5.2016
The latest release of GNATY contains the beta inclusion of the meta-alignment tool (presented at the ESHG 2016). This latest version is also based on the code GensearchNGS 1.6.00, which contains stability improvements to all existing tools.
Multithreading and p-values - 15.09.2015
A small maintenance release of GNATY has been made which includes by default the p-values of each variant in the output file. Other improvements to the VCF file format output have been made as well as the introduction of a new command line option for variant calling -threads, which allows to use multiple threads to call the variants in a BAM file. Please note that using more than 2 threads is unlikely to improve performance as GNATY is heavily I/O bound.
First release - 04.05.2015
Variant callingGNATY contains a variant calling tool that is based closely on the way Varscan 2 calls variants on BAM files. To run the variant calling with the default parameters on a sample BAM file, use the following command:
java -jar gnaty.jar caller -bam ALIGNMENT.bam -ref REFERENCE.fasta -out VARIANTS.vcfShow Varscan 2 and GNATY equivalence
The following GNATY command:
java -jar gnaty-1.0.jar caller -bam d1.bam -qbase 13 -rar -one -vs2 -freq 0.2 -cov 10 -allel 4 -ref data/hg19.fasta -out gnaty_D1.vcfis equivalent to the following Varscan 2 command:
samtools mpileup -x -B -R -C 0 -Q 13 -f hg19.fasta d1.bam | java -jar VarScan.v2.3.7.jar mpileup2cns --min-coverage 10 --min-reads2 4 --min-var-freq 0.20 --output-vcf 1 --strand-filter 0 --min-avg-qual 0 --p-value 0.99 --variants -o varscan2.vcf > varscan2.vcf
Many aspects of the variant calling can be fine tuned. Here is a list of parameters that can be used:
|Variant calling options|
Coverage analysisThe coverage analysis tool in GNATY is mainly replicating the coverage analysis tool found in BEDtools, creating a BED file containing the coverage information of a given BAM file. To create a BED file containing the coverage information of a BAM file use the following command:
java -jar gnaty.jar coverage -bam ALIGNMENT.bam -out COVERAGE.bedShow Bedtools2 and GNATY equivalence
The following GNATY command:
java -jar gnaty-1.0.jar coverage -bam d1.bam -out gnatyCoverageD1.bedis equivalent to the following Bedtools2 command:
genomeCoverageBed -ibam d1.bam -bg > bedtoolsCoverage.bed
The complete list of options can be found here:
DNAseq workflow in a diagnostic context, and an example of a user friendly implementation
Beat Wolf, Pierre Kuonen, Thomas Dandekar, David Atlan
BioMed Research International, 2015
GNATY: Optimized NGS variant calling and coverage analysis
Beat Wolf, Pierre Kuonen, Thomas Dandekar
If you use the software and detect potential bugs we would greatly appreciate a bug report via email.
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