Low coverage loci - GATK pipeline
Hi GATK team, I am posting this question for everyone's benefit as it will shed more light on how HaplotypeCaller and other GATK programs deal with low coverage positions. For the sake of this example,...
View ArticleProblem with HaplotypeCaller and GenotypeGVCFs
Hi just wondering if you have any experience with this problem. I am following GATK best practices for a targeted sequencing experiment. After the GenotypeGVCFs phase the majority of variants are...
View ArticleIs GATK overestimating the heterozygous calls?
Hi, I have 24 genotypes distributed in 4 different populations. I used HaplotypeCaller with the option –ERC –GVCF and obtained the vcf file for each genotype. Then combined all the genotypes to a...
View ArticleTruth or control samples - Variant calling
Are we able to incorporate truth/control samples in addition to dbSNP when calling variants with GVCF (cohorts) or the traditional way with HaplotypeCaller. There are for example situations where the...
View ArticleGenotype Called by HaplotypeCaller
Hello, I'm running GATK pipeline for Variant calling. First starting with...
View ArticleGENOTYPE_GIVEN_ALLELES mode not work in GATK4 beta
Hi, guys, I tried to run GGA(GENOTYPE_GIVEN_ALLELES) of GATK4.beta.1, but failed with NullPointerException, I'm sure that my input file and parameter settings are OK, cause I have checked my setting...
View ArticleHeterozygous X variants observed in male samples called by HaplotypeCaller in...
Hello GATK team, I have called variants with HaplotyeCaller in the whole exome data of 6 people (4 affected males and 2 unaffected). All 4 male patients are heterozygous for three variants in a gene...
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DP differences between haploid and diploid mode
I would appreciate some help in understanding better the differences between haploid and diploid mode when it comes to calling and joint-genotyping (HaplotypeCaller + GenotypeGVCFs) in gatk. In...
View ArticleVariant calling using a phased genome as reference
Hello, I want to do variant calling in a diploid organism using a phased genome as a reference. Therefore, in the reference we have both chromosomes represented. For variant calling with Haplotype...
View ArticleHC listing depth one read less
Hi, I ran haplotypecaller on a bunch of samples using the following commands: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -drf DuplicateRead -R hg19.fa -I SAMPLE.bam -o SAMPLE.g.vcf -L...
View ArticleUsage of "--dontUseSoftClippedBases" HaplotypeCaller option for exom...
Hi GATK Team, HaplotypeCaller does not call structural variants from soft clipped bases, therefore the "--dontUseSoftClippedBases" should mainly reduce false positives (e.g. incomplete adapter...
View ArticleJoint genotyping exomes is extremely slow (part of the germline...
I am enduring an incredible slow down during my genotyping stage of the haplotypecaller GVCF command series. It is my understanding from the documentation that this step should be rather fast: "This...
View ArticleSNV gets dbSNP annotation in one sample, doesn't get annotated in another one
Hello everyone, I recently run HaplotypeCaller for GATK3.7 on a series of samples (several GATK runs performed at the same time), using the latest release of dbSNP(150). This was the command line I...
View ArticlePhasing
Hi there How do u incorporate phasing with your variants if you dont have data from parents. my haplotype output is 1/1 not 1|1 so how can we say haplotyper can give phased haplotypes. Huma
View ArticleBiallelic variants only with HaplotypeCaller
I want to restrict the HaplotypeCaller to only call biallelic sites. I'm thinking that this can be accomplished with --max_alternate_alleles, although I'm not 100% whether this parameter should be set...
View ArticleMultithreaded HaplotypeCaller gives different GVCF files to single-core run
Hi, I've been recreating a bioinformatics pipeline for paired WGS data which largely follows the GATK best practices, but I'm having issues with HaplotypeCaller to create a GVCF file for one...
View ArticleSnpEff html and .vcf file result are not matching
Asslamu Alikum I have successfully managed to run SnpEff for my vcf files. However, the count of missense variants in my html file and the VCF file generated by SnpEff are different. Missense in HTML:...
View ArticleIs Indel realignment necessary when HaplotypeCaller re-assembles all reads in...
If HaplotypeCaller re-assembles all reads in a region Why is it recommend to run IndelRealigner first?
View ArticleIs there a paper describing the »Haplotype Caller algorithm?
Hi, I'd like to ask you if there is a paper describing the Haplotype Caller algorithm, if you could please send me the reference. I have tried to find it, but I only found the paper on GATK which is...
View ArticleDoes HaplotypeCaller detect SNPs which are heterozygous (not matching the...
Dear GATK team, I have a simple question regarding the HaplotypeCaller/UnifiedGenotype module. There are 3 options for SNPs in the output depended on the reference. Homozygous for the reference,...
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