Question for FisherStrand
Hi. I am trying to interpret the FisherStrand provided by GATK variant annotation. By using variant annotation tools in GATK, I made the vcf files annotated with FisherStrand. For my detected mutation...
View Articlejava.lang.ExceptionInInitializerError
I'v built gatk and mutect successfully(according to https://github.com/broadinstitute/mutect) but met this error. [root@ohpc-server target]# java -jar mutect-1.1.7.jar -h ERROR...
View ArticleASECounter
Hi, do you have any tutorial or documentation about how to use ASECounter in combination with vcf2diploid tool and 2-way STAR alignment? You mention this in the paper "Tools and best practices" but not...
View ArticleReferce SNPs in the same vcf file than the alternative alleles
Hi all, I have a simple question, I have several individuals sequenced with GBS and I want to call SNPs from all of them. Using the best practice approach, that includes to run the HC in GVCF mode and...
View Article2017 Feb workshop presentation slides and tutorial materials
These are the materials that we are presenting at the February 2017 GATK workshop in Leuven, Belgium. Materials Link DAY 1: GATK Best Practices talks Slide decks presented on Day 1 Google Drive Folder...
View ArticleERROR running SplitNCigarReads on RNAseq data using Ensembl Mus Musculus...
I was trying to run this commands ~/downloads/gatk-3.7 -T SplitNCigarReads -R ~/refFiles/Mus_musculus/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa -I...
View ArticleGenotype with depth but no coverage of either of alleles?
Hello I used Haplotypecaller, extracted SNP and did hard filtering. I can see genotype without allele coverage. I was wondering about the issue? Please check the last sample. Also, please check the...
View ArticleError I meet when install MuTect on a linux server
Hi, I am trying to install MuTect on a linux server. By the instruction, I did the steps: make a new source directory (e.g. mutect-src) mkdir mutect-src cd mutect-src get MuTect source git clone...
View ArticleRelease Notes for Oncotator version 1.3.0
Oncotator version 1.3.0 was released on July 24, 2014. This document lists the main changes that were made to the program. For more details about code changes, please see the source code on Github....
View ArticleHashMap iterator problem with GATK 3.6 on NA12878 validations
Hi all; I was running validations with the latest GATK 3.6-0 release and ran into an issue on NA12878 where a region around the centromere on X fails with a HashMap NoSuchElementException. I tried to...
View ArticleSNPs filtration and Prioritization
I have run Exome sequencing on 12 patients suffering from Renal failure. A bioinformatics team analyzed the sequencing data and generated a sheer load of SNPs and INDELS approximately (4000/patient)...
View ArticleSNP distribution across chromosome
Hi, I wonder to ask -is there any tool in the GATK to calculate SNPs/Indels distribution in each chromosome based on 100kb or 1 MB window size? Thanks.
View ArticleSomaticGenotypingEngine - At Locus chrchr8:129712469, we detected that...
Hi, I wonder what am I doing wrong with my input to MuTect2. java -Xmx16g -Djavaio.tmpdir=. -Xmx58g -jar GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T MuTect2 --num_cpu_threads_per_data_thread 16 -R...
View ArticlePicard CollectOxoGMetrics empty metrics
I tried to collect OxoG metrics, but less than 2% of my BAMs gave empty metrics as below. I have also updated my picard to 2.8.3. The example file I have is of normal size (14G). Also I saw from...
View ArticleHaplotypeCaller in GVCF mode for trio
Hello! I am setting up a GATK pipeline for analysis of trio. I have run all the step perfectly up to HaplotypeCaller, then GenotypeGVCFs, and finally PhaseByTransmission walkers. However, by manually...
View ArticleRelationship between depth and genotype?
Hi, I am new to WGS and would like to know how the genotype is attributed. It seems it does not depend much on depth of allele ratio. We ran GATK3.6 and Freebayes on the same BAM 50-50X files and...
View ArticleClik here to view.
Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticleCNVDiscoveryPipeline 2 Jobs Fail
HI, Iam running GenomeStrip (lattest version) locally in a Docker-Container with wdl. I can run SVPrepross without any errors for my samples. For saving time I run GenomeStrip only on Chr11/14. When I...
View ArticleUnifiedGenotyper error: Somehow the requested coordinate is not covered by...
Dear GATK Team, I am receiving the following error while running GATK 1.6. Unfortunately, for project consistency I cannot update to a more recent version of GATK and would at least wish to understand...
View Article">After running vcf-consensus command it showing< The sequence "21" not found...
Can anyone help me to figure out this issues....
View Article