Calling a complete set Germline+Somatic Mutations for a Cancer Sample
I need to produce a set of all DNA-level variants for cancer patients to serve as exclusion sites for RNA editing site finding. Currently have have matched Tumor-Normal WES data for these patients....
View Articledownsample_to_coverage in HaplotyperCaller
Hello, Here I have a question about downsample_to_coverage in HaplotypeCaller. I found -dcov cannot be used in HaplotypeCaller and I tried to change the values of parameters maxReadsInRegionPerSample...
View ArticleJoint analysis on germline SNP discovery between paired-samples
Hello, I have a cohort of several sibling pairs, and I am interested in finding Germline SNPs for each pair. Furthermore, I understand from the best practices that a joint analysis using the Haplotype...
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 ArticleError message during PhaseByTransition
Hi, I am running PhaseByTransition on a set of 250+ family trios. I am getting this error message: Sample lgsnd32563jz3 found in data sources but not in pedigree files with STRICT pedigree validation...
View ArticleCalculate Posterior Probability on Targeted Panel
Hello After hard filter a callset that is too small for VQSR I wanted to make sure that it is okay to still use CalculatePostProb on a targeted panels (i.e. 10-50 genes). James
View ArticleHaplotypeCaller/ Variantannotator no allele balance tag for all SNPs
Version 3.1.1. Human normal samples. I couldnt find AlleleBalance and AlleleBalanceBySample tags in my vcf outputs. Tags are not found even for single variant I tried HaplotypeCaller with -all or...
View ArticleOverview of Queue
1. Introduction GATK-Queue is command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often...
View ArticleMuTect2 tumor only mode: empty VCFs
Hello, I am trying to run Mutect2 in tumor only mode without a matching normal. However, when I did this, MuTect2 produced output VCFs that had a full header, but had no variant calls. Here is a sample...
View ArticleGenotypeGVCFs sees DP incorrectly in INFO, not FORMAT field
I have a potential bug running GATK GenotypeGVCFs. It complains that there is a DP in the INFO field, but in my haplotypecaller-generated -mg.g.vcf.gz's I do not have a DP in the info, I do have DP in...
View ArticleGATK on RAD Data - extraordinarily long run times
Hi all, I have Type 2B RAD data from many individuals from several populations of my non-model species, mapped using Bowtie 0.12.8 to a reference database made by extracting all potential RAD sites...
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(How to) Generate an unmapped BAM from FASTQ or aligned BAM
Here we outline how to generate an unmapped BAM (uBAM) from either a FASTQ or aligned BAM file. We use Picard's FastqToSam to convert a FASTQ (Option A) or Picard's RevertSam to convert an aligned BAM...
View ArticleWhat's the version of bwa being implemented in GATK4 bwaspark tool?
Hi, Is the bwa of the bwaspark tool is the latest 0.7.15 version or not? Thanks!
View ArticleMutSigCV gene covariates and full exome coverage, gene symbol discrepancies.
Hi, I observed this issue while analyzing a known dataset. Gene names in two files that MutSig uses (gene.covariates.txt and exome_full192.coverage.txt) are not according to HGNC and some of the gene...
View ArticleGenotype set to missing with lots of hom ref reads
In the following final VCF (produced by following the gVCF workflow) I get quite a number of positions reported as missing (1.2M out of ~24M bases). This of course isn't unexpected, however upon closer...
View ArticleA suddenly stop when running GenotypeGVCF.
The input script is like this: java -jar /nfs/home/gatk/GenomeAnalysisTK.jar -T GenotypeGVCFs -R /nfs/home/tool/gatk/bundle/2.8/hg19/ucsc.hg19.fasta --variant /home/sample/sample4/AD_1.g.vcf --variant...
View Articlejava.lang.ClassNotFoundException error when running FastqToSam in GATK4
Hi, Here is my log file, what does " java.lang.ClassNotFoundException: org.xerial.snappy.LoadSnappy" mean? Thanks Using GATK jar...
View ArticletrustAnchors mustn't be empty ...
I'm starting to get a weird warning message which appears four times at the end of any GATK command run as a qsub job on a Linux SGE. INFO 15:57:27,936 HttpMethodDirector - I/O exception...
View Articleincompatible reference and reads error when running GATK4 BwaSpark
The bam was created using FastqToSam, so it is unaligned. I think that's the reason why the read contig list was empty. Is there any solution for it?Thanks! Running:...
View ArticlePanel Of Normals for MuTect
I am wondering if there is a public repository from which one can build a panel of normals? A couple of questions about that: 1. Must all the sample for a PON come from the same platform? 2. if not, is...
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