Running HaplotypeCaller in GENOTYPE_GIVEN_ALLELES mode with...
Hi Sheila and Geraldine When I run HaplotypeCaller (v3.3-0-g37228af) in GENOTYPE_GIVEN_ALLELES mode with --emitRefConfidence GVCF I get the error: Invalid command line: Argument ERC/gt_mode has a bad...
View Articledownsample_to_coverage in HaplotyperCaller
Hello, Here I have a question about downsample_to_coverage in HaplotypeCaller. I found -dcov cannot be used in HaplotypeCaller and I tried to change the values of parameters maxReadsInRegionPerSample...
View ArticleJoint analysis on germline SNP discovery between paired-samples
Hello, I have a cohort of several sibling pairs, and I am interested in finding Germline SNPs for each pair. Furthermore, I understand from the best practices that a joint analysis using the Haplotype...
View ArticleGenotypeGVCFs sees DP incorrectly in INFO, not FORMAT field
I have a potential bug running GATK GenotypeGVCFs. It complains that there is a DP in the INFO field, but in my haplotypecaller-generated -mg.g.vcf.gz's I do not have a DP in the info, I do have DP in...
View ArticleGenotype set to missing with lots of hom ref reads
In the following final VCF (produced by following the gVCF workflow) I get quite a number of positions reported as missing (1.2M out of ~24M bases). This of course isn't unexpected, however upon closer...
View Articlewindow size in haplotypecaller's output bam
Hi, I am using HaplotypeCaller to re-align reads according to a set of pre-existing somatic variant calls. So far, this seems to work well; however, when I review the output bam in IGV, I notice that...
View ArticleGenotyping VCF with HC
Hi, I am using Haplotype Caller to genotype a VCF file. I am using this exact command line: java -Xmx20g -jar GATK/3.6-0-g89b7209/GenomeAnalysisTK.jar \ -T HaplotypeCaller -R $indexFasta -I $Bam -o...
View ArticleError with my HaplotypeCaller scala script
Hi everyone, I'm trying to run HaplotypeCaller through Queue because it really took a long time for HaplotypeCaller to finish one job. I've already read about some examples and forums to start on my...
View ArticleMESSAGE: Code exception (see stack trace for error itself)
Hi all, I meet some error while call variant with HaplotypeCaller, please help~~ Thanks a lot! my CMD: java -Xmx20g -jar GenomeAnalysisTK-3.6.jar -T HaplotypeCaller -R /human_g1k_v37_decoy.fasta -I...
View Articlewrong genotypes are not being corrected through genotype refinement
Hi, I am calling variants in a family and I have observed that some variants are being called homozygous although they are heterozygous because the second allele is present only in a very small amount...
View ArticleHET or HOM in RNA-seq calls with low allele frequency
I'm using the RNA-seq Best Practices pipeline to look at some of my data, and I'm seeing some calls that I'm having difficulty in understanding. An example site looks like this: A G 5178.77 PASS...
View ArticleHow to get heterozygotes SNP with HaplotypeCaller ?
Hi, I am new to GATK, I try to find SNPs for paired-end data in the mosquito. The genome of the mosquito many polymorphism. I try to get a VCF file for each position all posibility for a SNP. In fact,...
View ArticleErrors at the end of the SNP calling
Hi I am following the next steps to call variants in RNA-seq data: https://software.broadinstitute.org/gatk/guide/article?id=3891 I am runnig the step 6 of variant calling using this command line: java...
View ArticleHaplotype caller AF - How to obtain the real AFSpectrum.
Hi GATK team, I just figure out recently that the vcf I produced with HC was producing theoretical allele frequencies. But I would like to have an allele frequency per population (I can always...
View ArticleMultisample SNP Calling
Hello! I'm trying to use GATK to call SNPs on multiple bam files (at once) but I encounter some "problems". I tried HaplotypeCaller and UnifiedGenotyper and it works well. The vcf is generated. But not...
View ArticleHaplotypeCaller Error on some bam files
Hello GATK team, I report an error using HaplotypCaller on 3 bam files (other 34 bam files were processed without problem) Exemple: $ nohup /opt/java/jre1.8.0_102/bin/java -jar...
View Articleskip chromosomes GATK HaplotypeCaller
I am trying to use GATK HaplotypeCaller to identify variants on a set of bam files. however, my bam files contain only data on chrX, but the headers have the @SQ tag for all chromosomes, including the...
View ArticleHaplotypeCaller does not call variant depending on the interval list I use.
I am trying to explain why HaplotypeCaller calls a variant in some cases but not in others. I notice that a FN had very good coverage (>2000x) but wasn't being called. I ran HaplotypeCaller using an...
View ArticleBug in HaplotypeCaller: Lines meant to STDERR go to STDOUT
I use HaplotypeCaller v. 3.6-0-g89b7209. I want to compress the output before writing it to the disk and use command like this: gatk -T HaplotypeCaller ... -o /dev/stdout | grep -v -e --- -e WARN |...
View ArticleRecommended protocol for bootstrapping HaplotypeCaller and BaseRecalibrator...
I am identifying new sequence variants/genotypes from RNA-Seq data. The species I am working with is not well studied, and there are no available datasets of reliable SNP and INDEL variants. For...
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