Clik here to view.
Unboxing GATK4
This is one of two posts announcing the imminent beta release of GATK4; for details about the open-source licensing, see this other post. You've probably heard it by now: we are on the cusp of...
View ArticleERROR stack trace
I got an error when I was filtering variant "ERROR stack trace". This is the command I have used to filter. java -jar /home/sawannee/tools/GenomeAnalysisTK.jar -T VariantFiltration -R...
View ArticleVCF INFO annotation for non-variant sites
Hello, I am calling variants using HaplotypeCaller --> CombineGVCFs --> GenotypeGVCFs. To determine the accessible genome, I emit all sites in the last step and I want to get several INFO...
View ArticleInsertion Homozygous but heterozygous in BAM files
Hello, I have some troubles with insertion variation. In my VCF file it is flagged as homozygous (1/1) but on my BAM file it appears heterozygous. I generated BAM output file from HaplotypeCaller but...
View ArticleHow to use multiple g.VCF files in GATK4.beta.1 GenotypeGVCFs?
Hi, I tried to use GenotypeGVCFs from GATK4.beta.1, but there seems to be still a bug with the --variants statement. At first I gave a list of my g.VCF files to it (ending .list as it worked in...
View ArticleReference Confidence Mode
Hi Is a benefit of using joint genotyping in reference confidence mode a more accurate genotype for samples, especially non W Eurasians (when using NA 12878 as the reference) ?
View ArticleThere are 4 variant calls in g.vcf files that disappears in the VCF file.
Hi, When I run HaplotypeCaller on my files, the following four calls that are present in g.vcf but not in the vcf file. 1 116268178 . GAAAAA G,GA,GAA,GAAA,GAAAA,GAAAAAA, 329.70 ....
View ArticleReference for WGS
Would it be better to use an E Asian reference instead of NA 12878 when processing E Asian samples since calls are affected by the reference used?
View ArticleHaving trouble running GenotypeGVCFs with around 50 samples
Hi. I may be making a simple mistake but I cannot figure out what is going on at all. I am currently trying to run GenotypeGVCFs on around 50 whole human genome samples. These samples were produced...
View Articlequestions about downsampling
Hi, I am using HaplotypeCaller to call variants on targer region sequencing data, the mean coverage is about 600, I want to downsample my data to test the minumum mean coverage required for variant...
View Article[GATK 4 beta] StackOverflowError in running Mutect2
I wonder about an error in running Mutect2 in GATK 4.beta.1-14-g9d9ca1f-SNAPSHOT. Mutect2 seems to be complete successfully but unsure that what the StackOverflowError mean. Thank you! [July 10, 2017...
View ArticleProperly support secure communication with forum (HTTPS)
Dear GATK Support Forum administrators, The forum is available securely over HTTPS, but the browser shows several warnings because assets are included insecurely over plain HTTP. Could this please be...
View ArticleGATK v4 Variant Recalibrator command line
Could someone please provide me with a sample command line to run Variant Recalibrator for GATK v4? I am running the tool using GATK 4 Alpha with the following command line:...
View ArticleAlternatives to realignertargetcreator
Dear GATK-Team, Thank you very much for development of GATK4 under BDS license model. This is a very great progress! I have a question about Realignment under GATK4. As far as I know, the GATK3.7-tools...
View ArticleWhere can I find gsa-unstable?
@vdauwera comments in the GitHub merge/pull request #23. @ronlevine, Could you please make this tiny change in gsa-unstable? Where is that gsa-unstable repository or branch?
View ArticleCrashes with segmentation fault in shipped `libVectorLoglessPairHMM.so`
Dear GATK people, Our scientists reported, that GATK 3.6 and 3.7 terminates with a segmentation fault on a lot of Intel systems. Crazily enough, it’s not reproducible on all of them despite being the...
View ArticleClik here to view.
(How to) Call somatic copy number variants using GATK4 CNV
Presented tools are in BETA. Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section....
View ArticleStrategy low coverage ancient DNA- HaplotypeCaller
Has any staff member attempted to process low coverage ancient DNA (avg coverage <1) with low endogenous content using HaplotypeCaller. If so, what settings are suggested so as to minimize reference...
View ArticleClik here to view.
Picard haplotype map file format
The haplotype map that certain Picard tools require is a file that maps SNPs to LD (linkage disequilibrium) blocks. These tools include Picard CrosscheckReadGroupFingerprints and CheckFingerprint. For...
View ArticleLogging error when connecting to ftp server
Hello! i am trying to run the following command to download the dbsnp_138.b37.vcf.gz and i get a login erro. following my command and error message. am I making any mistakes or the server is having a...
View Article