Error with HaplotypeCaller
I have a bam file with duplicates removed. And I added the read groups using picard as: java -jar gatk/picard-tools-2.5.0/picard.jar AddOrReplaceReadGroups \ I=input.bam \ O=input.group.bam \ RGID=4 \...
View ArticleInclude VCF filename in the error message when VCF file format is not recognized
Hi, run RealignerTargetCreator but using multiple '-known file.vcf' arguments. One of the files is causing a problem. It is not very helpful message anyway: GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -T...
View ArticleError while running HC on ChrX
Dear GATK, I have a set of 4 bam files that I was able to generate genotypes from using HaplotypeCaller for Chr20. I took the same data and tried to call genotypes for ChrX, and received the following...
View ArticleHaplotypeCaller does not generate FS, QD annotations even when specifically...
It seems all recent GATK's HaplotypeCaller versions (versions 3.2 to 3.6, haven't tested older versions) miss to generate some of annotations like FS and QD (even when requested explicitly by...
View ArticleFiltering variants by depth of coverage using SelectVariants
I am trying to manually filter the results from HaplotypeCaller because my organism is anything but model. I sequenced 60 samples and had an average coverage of ~60X per sample across the genome. As...
View ArticleHaplotype caller BP_RESOLUTION :More AD values than alleles called for
My intention is to find different bases called in a particular chromosome location irrespective of it being assigned as SNP/badbase. I user the below command: java -jar 3.5/GenomeAnalysisTK.jar -T...
View ArticleNo varaint calling with Wgsim simulated reads
I have generated 1 million 600bp single ended reads using Wgsim read simulator from chr21 of hg19. All the bases have 40 base quality. The reads are aligned with BWA-MEM and then sorted and...
View ArticleVariant calling with multiple individuals and libraries.
I have multiple individuals. Let's say they are S1 (Subject 1), S2 and S3. There are two Chip-seq libraries for each subject (AC, ME). So I have 6 libraries in total. S1_AC, S1_ME, S2_AC, S2_ME, S3_AC,...
View ArticleVery long run-time - GATK HaplotypeCaller GVCF with Ion proton reads
I analyzing the proton reads using GATK Haplotypecaller. but I have an very long run-time to analyze this data with below command. gatk -Xmx48g -Djava.io.tmpdir=./ -T HaplotypeCaller -nct 8 -R...
View ArticleHow to determine heterozygosity (hets) parameter for non human?
Hello, I would like to run the Haplotype caller on 3 samples of yeast. Is there a recognized value for the heterozygosity parameter for yeast (such as 0.001 for human)? and where can I find post...
View ArticleSeveral Annotations not working in GATK Haplotype Caller
I am using Genotype Given Allele with Haplotype Caller I am trying to explicitely request all annotations that the documentation says are compatible with the Haplotype caller (and that make sense for a...
View ArticleHaplotypeCaller - different versions & code exception
Dear GATK team Now I am trying to run HaplotypeCaller to call SNPs on the realigned bam files from a poplar species, and use the genome of Populus trichocarpa as reference. The coverage of different...
View ArticleHaplotypeCaller Code exception & different version
Dear GATK team Now I am trying to run HaplotypeCaller to call SNPs on the realigned bam files from a poplar species, and use the genome of Populus trichocarpa as reference. The coverage of different...
View Articlehow I interpret the genotype result?
Dear all, Follow the GATK best practice, I got one sample with the genotype 0/0:47,0:49:99:0|1:131931451_TA_T:0,141,1807 in the vcf file. According to the format column GT:AD:DP:GQ:PGT:PID:PL, this...
View Articlesome questions about difference between HaplotypeCaller and MuTect2
Hi, Recently I have been worked in variant calling using GATK and I have some questions in the process of learning GATK tools. I’m interested in the essential difference between HaplotyepCaller and...
View ArticleGATK Runtime Error NullPointerException while running Haplotype Caller
Hello, I am trying to run the HaplotypeCaller and have run into a RunTime Error. I am using GATK version 3.5-0-g36282e4 I am running the command as follows: java -jar...
View ArticleHaplotypeCaller fails on joint calling of gVCFs
Hi, when I run HaplotypeCaller on on a bunch of .g.vcf files, at the joint discovery stage, it creates the output vcf with the header, but doesn't output the variants. There are a couple of warnings I...
View ArticleWhat is the source of the runtime error when using HaplotypeCaller?
Greetings, I am attempting to use the HaplotypeCaller using GATK version 3.6 and received a Runtime Error. The command I used was: Java –jar GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -R $chicken.fa \...
View ArticleMissed SNPs downstream of intronic repetitive context
I've found some interesting behavior in HaplotypeCaller in GATK 3.6 that I was hoping someone would help explain. I have a sequence context with 3 phased SNPs directly downstream of an intronic...
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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