When I call Indels from my vcf file using GATK analysis tools I ger an Error!
Hi I used the GATK pipeline until I got a vcf that had SNPs and Indels, so I used GATK Analysis tools to remove SNPs and keep Indels. But after adding the reference genome, dictionary and index I get...
View ArticleClik here to view.
(How to) Map and clean up short read sequence data efficiently
If you are interested in emulating the methods used by the Broad Genomics Platform to pre-process your short read sequencing data, you have landed on the right page. The parsimonious operating...
View ArticleGATK 3.7 to 3.8 migration problems creating/accessing temp files
We observed a strange behavior in the UnifiedGenotyper with GATK 3.8 that we didn't see using the previous version 3.7. All our scripts remain unchanged from comparing versions. Here is the command...
View ArticleClik here to view.
Problem using GATK4 GenomicsDBImport for joint calling.
Hi, I am trying to use GATK4 for joint-calling. I am calling variants by HaplotypeCaller in GVCF mode for three samples (HG002-3-4). I am using HaplotypeCaller parallelized using scatter-gather method...
View ArticleGenotypeGVCFs tool gives different output depending on the order of input GVCFs?
Hi, I have been using GATK GenotypeGVCFs tool (versions 3.5, 3.7 and 4.0). It has come to my attention that depending on the order of input GVCFs, the output slightly changes, i.e. the total number of...
View Article"recapseg_bed" should be "recapseg_tsv" in "gatk_cov_pull" ?
Hi, For "gatk_cov_pull" in Firecloud, the input file "recapseg_bed" should be a GATK-style tsv file based on manual of "CalculateTargetCoverage". So, "recapseg_bed" is a little bit misleading. Is that...
View ArticleIndelRealigner Crashing, Java Fatal Error
Hello GATK, I am receiving the following error when running this script: java -Xmx32G -Djava.io.tmpdir=/data1/home/nipm/arvin/tmp \ -jar /data1/APPS/gatk_nightly/GenomeAnalysisTK.jar \ -T...
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...
View ArticleAbout GenotypeGVCFs?
I run into a problem when running GenotypeGVCFs for dealig with population gvcfs. my command lines as follows: /scratch/gkm/software/jdk1.8.0_131/bin/java -Xmx4g -jar...
View ArticleShould I provide the exome target list (-L argu) even while calling gVCF file...
Hi, Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). I downloaded the exome interval list from Illumina's website. 1) Trimmed the raw...
View ArticleSegfault when running GATK 3.6 in a container
I'm using GATK on the DNAnexus platform, which can convert Docker images to the ACI format in order to run them. I have a Docker image that uses GATK 3.6 to call variants, which runs fine under...
View ArticleCRAM support in GATK 3.7 is broken
I have not been able to get GATK 3.7 HaplotypeCaller to work with CRAM files at all (it has a 100% failure rate so far with our whole genome CRAMs). Based on my analysis of the problem, I don't think...
View ArticleVariantRecalibrator Error
My task: task VariantRecalibratorSNPs { File Raw_VCF String CohortName String Chromosome File? Parallelization String? InbreedingCoeff Map[String, String] Paths Array[String] RuntimeParams command {...
View ArticleGATK4 StrandArtifact
Hi, Can you offer any guidance on how the Strand Artifact values are calculated in GAT4? Is there any recommendation on how they should be used? I am specifically looking at the SA_MAP_AF and...
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 ArticleThe error of the genomestrip's Svpreprocess
Hi,I'm just use the genomestrip to call the sv from pigs. I have 30 bams and then follow the introduction to prepare the reference file ,genomeMaskFile ,copyNumberMaskFile and ploidyMapFile files.But...
View ArticleClik here to view.
VQSR: low TiTv
Hi I'm trying out VQSR on a batch of 16 human whole genomes (~25-30x). I was wondering if someone could review the below profiles. It seems the false-positive rate is much higher than the GATK...
View ArticleMarkDuplicates out of Memory
Dear all, I have been using Picard MarkDuplicates function to mark the duplicate reads which is found to be utlizing huge amount of memory compared to the memory used by GATK in subsequent steps. I...
View ArticleClik here to view.
A dog, a ship and an algorithm that measures relatedness
What is beagle. Beagle is a type of dog known for its even temper and intelligence. It is also the name given to the ship Darwin sailed to the Galapagos (the H.M.S. Beagle), where he developed his...
View ArticlePicard Markduplicates Error: Value was put into pairInfoMap more than once
Dear all, I got an error when i use picard tools to mark duplicates my picardtools version 2.8.3 my sample: PE, one lane BWA + GATK get index of Ref bwa index /disk/BGI_jiangzy_humilis/BGI_j_humilis.fa...
View Article