Exit code 3 for HaplotypeCaller?
I am getting an exit code 3 for HaplotypeCaller version 4.1.2.0. I checked the command line output and the only thing I can see is this: WARN InbreedingCoeff - Annotation will not be calculated, must...
View ArticleHaplotyeCaller - non-variant block records in gVCF
Hi, I have generated a gVCF for an exome (with non-variant block records) from a BAM file belonging to the 1000Genomes data. I am using GATK tools version 3.5-0-g36282e4 and I have run the...
View ArticleDifferent HaplotypeCaller variant calls based on Java version?
Hi, we are running HaplotypeCaller on two different Linux servers and getting slightly different VCF calls (only with SNVs, not Indels) with identical BAM files despite using the same script and having...
View ArticleUsing HaplotypeCaller for human samples, should I set the ploidy for non...
I've been working on the basis that this complexity is automatically handled by the algorithm, but i'm not sure. My question specifically relates to HaplotypeCaller in GATK4.
View ArticleI have tried creating a GATK project in the IntelliJ IDE as documented in...
It is giving error "error: package com.sun.javadoc does not exist final com.sun.javadoc.ClassDoc classDoc" everytime I run debug 'GATK debug'. Please help me
View ArticleGATK HaplotypeCaller MIXED variants delins
Hello GATK team ! I am facing a problem that I am not exactly sure your caller can address and I would need your opinion on that. I use GATK last version (3.4.46) haplotypeCaller to call my variants...
View ArticleRunning HaplotypeCaller on a multi-lane sample
Hello, I am interested in running HaplotypeCaller for a multi-lane sample. What is the best way to do this? I followed the protocol here...
View ArticleWhy does haplotype caller produce a vcf with per-lane output?
I'm using gatk4, I have input data for a single sample across four different lanes: v02_L1.fastq.gz v02_L2.fastq.gz v02_L3.fastq.gz v02_L4.fastq.gz I want to merge this into per sample results....
View ArticleNumber of Snps differ between individual GVCF files and final vcf file
I have total 96 gvcf file with respective number of variations 190 176 213 201 156 11 201 191 168 138 189 183 197 203 188 192 192 139 145 37 198 205 162 202 133 146 175 137 157 198 162 174 204 109 200...
View ArticleWhat is the current recommended practice for interval padding?
In the GATK Best Practices WDL in github, the GenotypeGVCFs commandline does not specify any interval padding via -ip or --interval-padding parameter....
View ArticleHelp understanding genotype in spanning deletion notation
Hello, I am working with a collaborator who had sequencing and variant calling done at the Broad. The resulting multi-sample VCF has spanning deletion notation. I am trying to understand what the...
View ArticleBest strategy to "fix" the Haplotype Caller - GenotypeGVCF "missing DP field"...
Hi, I've run into the (already reported http://gatkforums.broadinstitute.org/dsde/discussion/5598/missing-depth-dp-after-haplotypecaller ) bug of the missing DP format field in my callings. I've run...
View ArticleHow to add sample names in VCF?
I am using GATK best practices for germline SNPs and Indels 4.1.2.0. After mapping and recalibration, I run haplotypecaller in GVCF mode. I am combining all vcf files (output from haplotypecaller)...
View ArticleHow can I debug and develop the algorithm in GATK ,such as haplotypecaller,...
Is there any paper or documents ? and those test data where i need download,such as NA12878.HiSeq.b37.chr20.10_11mb.bam.
View ArticleCombineGVCFs performance
I've got 300 gvcfs as a results of a Queue pipeline, that I want to combine. When I run CombineGVCFs (GATK v3.1-1) this however seems fairly slow: INFO 15:24:22,100 ProgressMeter - Location...
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