Using JEXL to apply hard filters or select variants based on annotation values
1. JEXL in a nutshell JEXL stands for Java EXpression Language. It's not a part of the GATK as such; it's a software library that can be used by Java-based programs like the GATK. It can be used for...
View ArticleJava versioning changes and the future of the compatibility
I have a question regarding this issue. Oracle decided to start issuing rolling releases every 6 months to java virtual machine. Current tools work with Java 1.8 (A.K.A. Java 8.0) however I am...
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Haplotype caller not picking up variants for HiSeq Runs
Hello, We were sequencing all our data in HiSeq and now moved to nextseq. We have sequenced the same batch of samples on both the sequencers. Both are processed using the same pipeline/parameters. What...
View ArticleWhy am I getting this error when running GetPileupSummaries?
The code: gatk GetPileupSummaries -I V2.bam -V annot.vcf.gz -O getpileupsummaries.table The error: 11:13:10.829 INFO GetPileupSummaries - Initializing engine 11:13:11.515 INFO FeatureManager - Using...
View ArticleWhat is the GATKReport file format?
A GATKReport is simply a text document that contains well-formatted, easy to read representation of some tabular data. Many GATK tools output their results as GATKReports, so it's important to...
View ArticleHow to import GATK reports into Python/pandas DataFrames
Answering my own question. I searched around and could not find a Python equivalent to the gsalib R library, which enables R analysis of GATK reports produced by VariantEval and other tools. So I...
View ArticleDoes GATK4 Mutect2 support Force Calling?
Hi, Does GATK4 Mutect2 support Force Calling? If yes, could you let me know how to do it? Thanks a lot! Thanks, Chunyang
View ArticleVariantRecalibrator Engine failure
Hi, I'm trying to run the following on WGS samples: /gatk/build/install/gatk/bin/gatk VariantRecalibrator -R...
View ArticleBest practice germline variant calling hg19 on Firecloud
Hello, I noticed that the five-dollar-genome-analysis pipeline on FC is exclusively meant for use with an hg38 reference. Is there an equivalent for hg19? Thanks, Eric
View Article(Howto) Run GATK4 in a Docker container
1. Install Docker Follow the relevant link below depending on your computer system; on Mac and Windows, select the "Stable channel" download. Run through the installation instructions and initial setup...
View ArticleHow to properly merge bamouts after Mutect2
Hi, I ran Mutect2 (gatk4) using the -L command to split by chromosome, and the -bamout option. I am now using CatVariants (gatk3) to merge all the vcf files (one per chr) into a final vcf. And I also...
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Over estimation of AF in Mutect2 (GATK 4.0.2.1) ?
Hi, I ran Mutect2 (GATK 4.0.2.1) followed by FilterMutectCalls with default parameters. I got some passed variants with AF much larger than the alt_depth/total_depth (see attached image), I checked the...
View ArticleUnable to determine status of job ID error
Hi, I occasionally get the following type of error when using genome strip CNVDisvovery pipeline on a cluster running SGE, it will run successfully for long periods of time and then arrive at this type...
View Article"Unable to determine status of job" warn in Genome STRiP preprocessing
So when in the preprocessing step, there always occurs such kind of warning: WARN 10:50:19,392 DrmaaJobRunner - Unable to determine status of job id 2231784 org.ggf.drmaa.DrmCommunicationException:...
View Article(howto) Recalibrate variant quality scores = run VQSR
Objective Recalibrate variant quality scores and produce a callset filtered for the desired levels of sensitivity and specificity. Prerequisites TBD Caveats This document provides a typical usage...
View ArticleIs it possible to merge the multiple samples within a vcf file?
Greetings from Australia, Could someone please help me with this? I got a single vcf file containing 14 samples at the end of the best practices pipeline. For a bulk segregation analysis, I would like...
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Inconsistent results with HaplotypeCaller on haploid organism
Hello GATK team, I would appreciate some help in understanding how GATK works in GVCF mode on my data. Here is my data example I'm usign GATK v3.8: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 328-16...
View ArticleGenotypeGVCFs shows flag despite all reads in all samples supporting the...
Hello, I have been jointly genotyping variants in my samples using GenotypeGVCFs but a few sites show a flag despite all reads in all samples supporting the reference allele. Do you know why this might...
View ArticleCalling variants on whole exome and whole genome samples together?
Hi, I have 15 affected samples. 2 are whole exome and 13 are whole genome. They have already been realigned on a single-sample level and had BQSR performed. I am contemplating running UnifiedGenotyper...
View ArticleCross comparison between Array and NGS data
Dear GATK staff, I have a 11 samples that were sequenced using NGS (Illumina HiSeq) and 2 of these samples were also genotyped using an Illumina Human Global screening array (Illumina Iscan). I was...
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