Obtaining read group information from the fastq files
I have fastq files with headers @SN963:294:C847FACXX:1:1106:1077:2087 1:N:0:AGGCAGAA (File name -DYP26_blood_S3_L001_R1_001.fastq) and @SN963:294:C847FACXX:1:1106:1077:2087 2:N:0:AGGCAGAA (File name-...
View ArticleHaplotypeCaller raises an error with -A BaseCountsBySample
Hi GATK team , FYI I'm getting the following error with GATK 3.7: java -X -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta --validation_strictness LENIENT -I .bam.list \ -o...
View ArticleMutect2 problems on nct parameter
Dear All I use GAtk 3.6 an I sue Mutect2. I have a dell wiht 16 cpu with 50G of ram. [mre@compute-00-00]$ java -version java version "1.8.0_101" Java(TM) SE Runtime Environment (build 1.8.0_101-b13)...
View ArticleisCalled, isNoCall, and isAvailable in Genotype Filtering
Greetings, The VariantFiltration documentation mentions the availability of isCalled, isNoCall, and isAvailable methods in genotypeFilterExpression. I find it quite misleading because filters are...
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Calling variants in RNAseq
Overview This document describes the details of the GATK Best Practices workflow for SNP and indel calling on RNAseq data. Please note that any command lines are only given as example of how the tools...
View ArticleToo few indels for VQSR in Joint analysis of 75 exomes
Hi, I am trying to execute the pipeline for joint analysis of 75 exomes. I guess it is a reasonable number to use for VQSR but I have the well known problem with the too few INDELs. After the...
View ArticleOut of space when running SplitNCigarReads
I know this question has been asked before. I have read the answers of previous post and did fix by the instructions, but this problem keeping occur. I have checked my storage space, there is enough...
View ArticleMuTect v1 or Mutect v2?
Hi! I downloaded the cosmic file b37_cosmic_v54_120711.vcf, but still I had an error after running MuTect v1. Should I still go through liftover and filtering process this later file? Or best, I am...
View ArticleSelectVariants -selectType SNP
Hello GATK-team, I have called variants from whole genome Illumina data for each of seven individuals separately using GATK's HaplotypeCaller v.3.5 (with default options) and have then jointly...
View ArticleGATK4 exome runtime
Does anyone know what a typical runtime is for an exome alignment using GATK4 is?
View ArticleHomozygous
Dear GATK team, I wonder why GATK calls the following snp as homozygous: chr2 1609114 . T C 1874 ....
View ArticleCalculating Coverage Allele Threshold Using .wig file
Dear Broad Institute, Utilizing igv and igvtools, we were able to create a wig file using a bam file. However, if we want to be able to calculate the sum of mismatch qualities, is there a way to...
View ArticleHow does VariantEval's CountVariants option determine MNPs?
Hi, I am trying to understand what CountVariants is calling as an MNP in my dataset. When I run CountVariants, I get ~3K MNPs called across my samples. However, when I run SelectVariants with...
View ArticleDifferences between HaplotypeCaller and UnifiedGenotyper
Dear all I’m a little bit lost about differences in calling results using HaplotypeCaller or UnifiedGenotyper I’ve a bam generated from SureSelectV5 sequencing results in Illumina I’ve aligned...
View ArticleWeird trench plot from VQSR
Hi, I have used VQSR for a set of 308 individuals from targeted sequencing array (21MB) and the while looking at the plots, I was not sure if VQSR has worked properly. I am running VariantEval right...
View ArticleMuTect2: ERROR MESSAGE: Somehow the requested coordinate is not covered by...
Hi guys, I use mutct2 to do somatic variant calls, and got this ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions? I searched the forum and found people got...
View Article-nct >1 then PairHMM disabled
When I'm parallelising HaplotypeCaller (-nct 16) the PairHMM is disabled: PairHMM - Performance profiling for PairHMM is disabled because HaplotypeCaller is being run with multiple threads (-nct>1)...
View ArticleUnderstanding -nct and -nt
I am trying to understand GATK's parameters for parallelism: -nt / --num_threads controls the number of data threads sent to the processor -nct / --num_cpu_threads_per_data_thread controls the number...
View Articleerror running RNA-SeQC
Hello, I tried to run RNA-SeQC but got the following error: RNA-SeQC v1.1.8.1 07/11/14 Creating rRNA Interval List based on given GTF annotations Retriving contig names from reference contig names in...
View ArticleSpeed up HaplotypeCaller on IBM POWER8 systems
We all know how HaplotypeCaller and Mutect2 analyses can take a long time. IBM is now providing a native implementation of the PairHMM algorithm that leverages the new hardware available in their...
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