Heterozygosity
Heterozygosity in population genetics In the context of population genetics, heterozygosity can refer to the fraction of individuals in a given population that are heterozygous at a given locus, or the...
View ArticleAlternate allele filtering?
Hello, I am trying to call Het as: Ref allele 10-90% or Alt allele 10-90. I have four samples. If one sample is Het, that location is preserved if criteria for Het (as earlier) and Homozygous (> 90%...
View ArticleI've got some Intel for you right here
Here's the scoop. We've been working with Intel engineers for some time now, and we've all been enjoying it so much, we decided to commit to the relationship big time. As announced in this Broad press...
View ArticleError installing GATK: Exception in thread "main"...
Hi, I was trying to install GATK but when I try to run: java -jar GenomeAnalysisTK.jar -h I get the following error: Exception in thread "main" java.lang.UnsupportedClassVersionError:...
View ArticleRNA-seq and WGS for cancer samples (no paired T-N)
Dear GATK Team, I want to do SNP calling on cancer RNA-seq data (no matching normals). In some cases I have matching WGS data (for which I also want to do SNP calling) - but not for most cases. If I...
View ArticleGATK and MuTect licensing moves to direct-through-Broad model
We have some important news to share with you regarding the licensing of GATK and MuTect. The licensing agreement between us and Appistry will end effective April 15, 2015; from that point on, the...
View ArticleWhich training sets / arguments should I use for running VQSR?
This document describes the resource datasets and arguments that we recommend for use in the two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration), based on...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
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WDL building blocks: A tour of resources for pipelining with WDL
You may have noticed we’ve been talking about this new thing called WDL--the Workflow Definition Language. We've published a tutorial using WDL to run some GATK tasks, as well as a pipeline...
View ArticleBaseRecalibrator - Input files knownSites and reference have incompatible...
I am trying to use GATK BaseRecalibrator but I get this error: "Input files knownSites and reference have incompatible contigs" details: " ##### ERROR MESSAGE: Input files knownSites and reference have...
View ArticleFilterSamReads
Hello, I have a problem to run FilterSamReads and I don't know exactly how to resolve it: I have an input bam file (inputsorted.bam) and I want to filter it using this command: java -jar picard.jar...
View ArticleSAMtools bam_sort_core truncated file.
using samtools-1.3.1 getting error about bgzf reads samtools sort -n -m 4G --threads 4 -o out.bam xxx_hg19_Illumina_gdc_realn.bam [E::inflate_block] inflate failed: invalid distance too far back...
View ArticleHaplotypeCaller is calling thousands of variants that don't seem to be there
I'm baffled as to what might be wrong here. I use several different callers and downstream I try to locate each called variant in an mpileup. GATK produces thousands of variants for which my code...
View ArticleGATK stalls on particular NCBI reference genome
Hi, I am upgrading my analysis pipeline from GATK 3.3-0 to 3.6-0 on a CentOS 6.x machine and came across a problem with GATK stalling at the following point in the output below (I know that it is not a...
View ArticleGenotypeGVCFs multithread not working properly
Hi GATK team, I ran the haplotypcaller on a single mapped bam file. Command: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I MyMappedSample.bam --emitRefConfidence...
View Article(howto) Recalibrate base quality scores = run BQSR
Objective Recalibrate base quality scores in order to correct sequencing errors and other experimental artifacts. Prerequisites TBD Steps Analyze patterns of covariation in the sequence dataset Do a...
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Attend or host a GATK workshop to see what's cooking
GATK workshops bring you the latest in our methods development. The materials we prepare for workshops often serve as a base for our documentation on new or improved tools and workflows. So not only do...
View ArticleOncotator Error -- Please help me
I am running Oncotator 1.8.0.0 on MuTect2 output .vcf file. I did perform filtering for PASS before running Oncotator. If I run this on command line: oncotator -v --input_format=VCF --output_format=VCF...
View Article1000G Indels for BaseRecalibrator
Hello, I was searching for all the recommended sets of known sites for the hg38 reference version. As part of the recommendations, the 1000G indels is one of the input files for BQSR, but it is not...
View ArticleDepth of coverage on an exome
Hi, Apologies, I think this has been asked in a number of ways previously (http://gatkforums.broadinstitute.org/gatk/discussion/1831/depth-of-coverage-only-first-gene-summary-output) but I am hoping...
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