How download old GATK versions?
Hi, I am using a server with java version "1.7.0_45", could you send me the GATK compatible for this java? Where can I download the old GATK versions? Thank you, Matias
View ArticleI/O error loading or writing tribble index file, ONLY on mounted folders...
Hi, I am a bit stuck here. Any GATK tool I try (v3.5 and v3.7) that autocreates an index (e.g. ValidateVariants) fails in doing so with the following message: MESSAGE: I/O error loading or writing...
View ArticleGVCF from HaplotypeCaller using BAM with or without IndelRealignment+BQSR
Hi, I am studying why PDF figures from VQSR recalibration (https://software.broadinstitute.org/gatk/documentation/topic?name=methods#methods39) of my human exomes seem messy...
View Articlemissing samples after CombineGVCFs
Hi, I am working on the analysis of 180 exomes, (60 trios). To avoid memory problems, I'm combining the individual gvcf files into 3 cohorts of 20 trios (60 exomes). Then, I genotype the 3 cohorts...
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Version highlights for GATK release 2.6
It's finally summer here in New England -- time for cave-dwelling developers to hit the beach and do the lobster dance (those of us who don't tan well anyway). We leave you with a new version of the...
View ArticleWhat's in the resource bundle and how can I get it?
NOTE: we recently made some changes to the bundle on the FTP server; see the Resource Bundle page for details. In a nutshell: minor directory structure changes, and Hg38 bundle now mirrors the cloud...
View Article(howto) Use Oncotator on the Broad servers
This information is specific for using Oncotator at the Broad. This includes running Oncotator on the cluster and configurations used specifically at the Broad. Please note: if you are working on the...
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Should I analyze my samples alone or together?
Together is (almost always) better than alone We recommend performing variant discovery in a way that enables joint analysis of multiple samples, as laid out in our Best Practices workflow. That...
View ArticleGenotypeGVCFs: WARNING: of INFO fields not parsing
The HC calls in issue were called in a complete GATK 3.6-0/ JDK 1.8 workflow as follows: java -Xmx64G -jar $GATK_JAR -T HaplotypeCaller -ERC GVCF -R $REFGENOME -I $INPUT_FILE -o...
View ArticleGenotypeGVCFs --useNewAFCalculator -G Standard -G AS_Standard crashing with...
Hi, when running GenomeAnalysisTK.jar -T GenotypeGVCFs -nt 16 -R hs38DH.fa --dbsnp 00-All.vcf.gz --useNewAFCalculator -G Standard -G AS_Standard -o mysamples.AS.raw.vcf --variant...
View ArticleCombineGVCFs Error - Features added out of order
Hi GATK team, I am running the best practices pipeline on a large set of WES data. On some of the CombineGVCFs steps I am getting errors with the GATK v3.5. Here is the command: java -Xmx51200m -jar...
View ArticleUnexpected genotypes in GenotypeGVCF output
Hello GATK Team, I have 21 bam files that I ran through HaplotypeCaller in GVCF mode followed by GenotypeGVCF, using Version=3.4-0-g7e26428. I found a few entries that I am having a difficult time...
View ArticleHow should I pre-process data from multiplexed sequencing and multi-library...
Our Best Practices pre-processing documentation assumes a simple experimental design in which you have one set of input sequence files (forward/reverse or interleaved FASTQ, or unmapped uBAM) per...
View ArticleCustom Walker That Calls Other Walkers?
Hello, We're trying to make a tool that takes the output of several iterations of VariantEval (each stratified differently), and then uses these data to make another report. It would be very convenient...
View ArticleCalling RNAseq variants using a transcriptome FASTA
I know Best Practices recommends calling RNAseq variants based on the genomic fasta and BAMs with genomic coordinates. With the GENCODE references, it is also possible for us to call variants on a...
View ArticleCatVariants require all -V's to have the same INFO keys?
I called somatic SNVs with MuTect and somatic INDELs with MuTect2, and then attempted to use CatVariants to combine them into one file for downstream processing. However CatVariants will always break...
View ArticleVariantFiltration bug in 3.7? ' input string: "7.902" '
Hello, While trying to filter a file in version 3.7, I got a strange error: INFO 19:05:58,582 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 19:05:58,582 ProgressMeter - |...
View ArticleMemory setting issue in CNV calling pipeline step 2: SVAltAlign
Hello, I failed in running CNV calling step 2: SVAltAlign, probably because of the memory setting issue. Even though the "-lsfMemLimit 128" is specified in the command, which is: "java -Xmx128g -cp...
View ArticleGoogle Genomics - problem with regions/zones settings
While trying to run the GATK example at https://cloud.google.com/genomics/v1alpha2/gatk I get the following error Unsupported key/value pair in WorkflowOptions: defaultRuntimeOptions ->...
View ArticleConcatenated fastq files to vcf format
Hello! I have had blood samples of a dozen patients with breast cancer. Each sample was sequenced several times. And so there is several FASTQ-files for the each sample. Next, the files corresponding...
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