Could you please let me know any tool, to concatenate the gvcf files? Or...
Could you please let me know any tool, to concatenate the gvcf files? Or there is any other solution to run the intermediate HaplotypeCaller in GVCF mode on parts of the chromosome to speed up the...
View ArticleNo variants found by HaplotypeCaller
I have human RNA-seq data: paired-end reads (2x150bp) aligned with STAR. I tried to run HaplotypeCaller with usual parameters: `gatk HaplotypeCaller -R GRCh38.primary_assembly.genome.fa -I...
View ArticleHow to create a Haplotype file from HaplotypeCaller
I am new to use GATK4. I would like to generate a Haplotype file (.bam or vcf file with haplotype information). I followed the Best Practice step till haplotypecaller. REF="refs/ucsc.hg19.fasta"...
View ArticleWhy a variant site is listed in a GVCF run on a single sample, with no reads...
I have read couple documents on GVCF but still can't understand how it works. Just one example from the GVCF file I got from HaplotypeCaller from a single bam file with `-ERC GVCF` option: ``` chr22...
View ArticleHow do we know the stretch of variants that have been phased using haplotype...
I am using the following command to run haplotype caller /opt/apps/gatk/4.2.1/gatk HaplotypeCaller --dbsnp /home/dhwani.dholakia/archive/files_required_for_exome_analysis/dbsnp/GRCH37.p17_refseq.vcf -R...
View ArticleRegarding different genotype calls for same sample using Unified Genotyper &...
Hello Team, I am doing multi sample cohort exome analysis for which i have called SNPs using both callers (UG & HC).For one of my important SNP, i am observing different genotypes in few samples...
View ArticleMapping a locus to a chromosome in a genome
Hello I am currently working on a maize mutant and wild type data. I have the DNA-Seq data for these samples and I am currently using the GATK pipeline to analyze the data. I am trying to map the...
View ArticleHaplotype caller active regions parameters not available in GATK4
I would like to know like GATK 3.6 there was an option to define active regions, is there any option in GATK v4.2.1 The Active region parameters can be seen from this link:-...
View ArticleHow to analyze separately called gVCFs?
I have VCFs from a WGS experiment on several thousand subjects. I did not process the data through the GATK pipeline myself and have no access to the original BAM files or intermediary files. Each...
View ArticleHaplotypeCaller error: Badly formed genome unclippedLoc: Query interval is...
Hi there, I'm running the GATK best practice pipeline (locally on a Linux server without using docker) for Germline short variant discovery (SNPs + Indels) using the Generic germline short variant...
View ArticleAD allele depth interpretation
Hello, I have a query on the interpretation of the AD variable in a vcf generated by calling about 800 samples together. The header defines it as: ##FORMAT= and the forum further elaborates: AD is the...
View Articleunderstand HaplotypeCaller output vcf format
Hi there, I am using GATK4.1.0.0 version on germline pair-end illumina WGS data with following command: ``` gatk4.1.0.0 --java-options '-Xmx5G' HaplotypeCaller -R...
View ArticleRegarding optimal size of gvcf file generated by Haplotypecaller
Hi everyone, I am running Haplotypecaller to generate individual gvcf files of 50 samples of Cattle (Bos taurus) after removing Illumina adapters from 30x raw reads with ~ 120 bp read length....
View ArticleAre there runtime measurements of the HaplotypeCaller with the PairHMM FPGA...
Hello. I would like to know if there are runtime measurements of the HaplotypeCaller with the "--pairHMM EXPERIMENTAL_FPGA_LOGLESS_CACHING" option against other options such as "--pairHMM...
View ArticleThrowing Error: Invalid or corrupt jarfile while using GATK wrapper version...
Hello All, I am using GATK wrapper version: gatk-4.1.2.0, and while trying use it on HaplotypeCaller tool as following, ./gatk HaplotypeCaller --help it is throwing the following error message, Error:...
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Can I disable local reassembly and realignment?
Hello, I want to dentify short variants in RNAseq data. But I find HaplotypeCaller introduces many unusual alignments (see the raw bam and bamout file). Can I disable local reassembly and realignment...
View ArticleThe bamout file results are inconsistent with the VCF file results
Hi, I use GATK4 were analyzed, and found that took place on a site of "bamout" file multiple mutations, respectively from G mutation is T, the number of reads supported mutation is 14, and from G...
View ArticleGATK 3.8: genotype called as HOM_VAR while there is a large number of REF and...
Hi the GATK team, there is a mutation in my (haloplex) bam that was called (REF=C) as HOM_VAR in my bam while there are only a few reads carrying a ALT=A $ samtools mpileup -r "15:42171531-42171531"...
View ArticleForce skip INDELs in GATK output
Dear GATK, I ma using GATK4, my syntax is: gatk HaplotypeCaller -R $reference -I in.bam -ERC BP_RESOLUTION --max-alternate-alleles 1 -O out.raw.snps.g.vcf -L $SNP_TARGET In some regions i have curious...
View Articledetail information for --minimum-mapping-quality option in HaplotypeCaller
Hi, I posted the same question by adding the comment to a different post, but I couldn't get the answer yet, so let me post the same one here. I'm using HaplotypeCaller to find variants, however, could...
View ArticleHaplotypeCaller single sample mode error
Hello, I am trying to run GATK4 HaplotypeCaller on a bam file from a single individual on Ubuntu 18 with gatk HaplotypeCaller -R Tse_SBAPGDGG_D.fa -I AHP2746_sorted_dedup.bam -ERC GVCF -O AHP2746.gvcf...
View ArticleBAM with hight depth : variant called as HOM_VAR but there are almost no ALT...
Hi GATK Team, I'm using 4.1.2.0 / HaplotypeCaller with the following command with a Haloplex BAM (high depth) gatk --java-options "-Xmx5g -Djava.io.tmpdir=." HaplotypeCaller --minimum-mapping-quality...
View ArticleVQSR filtering and dbSNP
Hi, For VQSR filtering, it's assumed that all calls made by HaplotypeCaller or MuTect2 are put into VQSR? Polymorphic sites should only be culled AFTER the vcf is annotated with VQSLOD scores, and a...
View ArticleHow can I force HaplotypeCaller to call a genotype -- want to avoid gt=./.
In a single sample vcf I have homozygous snp that is not assigned a genotype, the genotype is missing (gt=./.). What knobs can I turn on HaplotypeCaller (in GATK 3.8 or 4.1.2) to assign a genotype to...
View ArticleBeginner's question: Why can't I start the analysis run on Terra?
Hello. I am new in genomic analysis and GATK. I am trying to start Haplotypecaller workflow on Terra. I have uploaded aligned genomic reads (bam file and bam index) and used appropriate genome assembly...
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Variant Caller and BAM file INFO not matching
Hello, I am using gatk-4.0.3.0 following the Best practices. BWA-> Picard Mark Dup -> GATK Base Recalib/Apply -> HC variant calling per sample For one of our samples, we have a variant called...
View ArticleGVCF of amplicon sequencing
Hi, I'm trying to generate a GVCF with HaplotypeCaller based on amplicon (PCR) sequencing, and bases towards the end of the reads (~10 bases last bases) consistently get genotype quality of 0, even...
View ArticleGatk haplotype caller java error
Hello GATK team, I am trying to run gatk haplotypecaller (version 4.1.1.0) on a bam file and used the following command: "java -jar /ufrc/gatk-4.1.1.0/gatk-package-4.1.1.0-local.jar -T HaplotypeCaller...
View ArticleShould I use GATK haplotype caller/unified genotyper for finding SNPs in 2...
I have two whole genome sequenced bacterial samples. I have their contigs file with me. I would like to pairwise comparison between isolate1 and isolate2 to identify SNPs between them. Should I use...
View ArticleAll ALT fields are the same after GenomicsDBImport and GenotypeGVCFs
Hi GATK team, I'm running GATK 4.1.3.0 to perform targeted single-cell genotyping, where each sample in the output VCF is a single cell (10-20k samples total per VCF). I've noticed something strange in...
View ArticleEmitting variants with low mapping quality
Hello, I am validating a new exome sequencing analysis pipeline using in-house-generated data from sample NA12878 and the Genome in a Bottle high confidence calls for this sample. I am using GATK...
View ArticleHaplotypeCaller generate incorrect heterozygous Calls
Hi, We have used GATK 3.6 and GATK 4.1 haplotype caller, to generate the variants, unfortunately, we are getting lots of incorrect heterozygous calls. Even only one read supports the variant it is...
View ArticleHow to get a smaller list of deNovo SNPs between 3 genotype
Hello. I am currently working on maize whole genome dataset and I have 3 samples- WT, MT and B73. I obtained the VCF files for all 3 datasets using the haplotype caller. However, the list of SNPs that...
View ArticleGATK Exception in HaplotypeCaller
Hi, I am using gatk 4.0.8.1 HaplotypeCaller for making g.vcf. I am running follwing command gatk --java-options "-Xms24g -Xmx48g" HaplotypeCaller -R new_hg38.fa -I S11_.sorted.BQRC.bam -O S11.g.vcf -L...
View ArticleWhat exactly is DP and how filtered is it?
I have read somewhat contradictory things across the documentation as to what DP actually measures, and I can't quite tell if I'm missing some distinction between the "different" DPs. I have read that...
View ArticleHow can a homozygous reference 0/0 genotype (GT) have a heterozygous phased...
Dear GATK support team, Multi-sample variant calling files made with GATK4 have both genotype, genotype phase and genotype phase block information....
View ArticleDiscovering singletons with GenotypeGVCFs?
Hi, I have several samples that I ran HaplotypeCaller (in normal mode) with that I am looking to discover germline variants from. I read that GenotypeGVCFs isn't good with discovering singletons, and...
View Articlenon-reference allele didn't be called into vcf by HC
Hi GATK team I ran HC joint calling and found out that some non-reference alleles didn't appear in the vcf. Most of these allele seems to reside on the region of relatively poor alignments. My first...
View ArticleHow does MAPQ affect haplotypecaller during germline calling
I understand that, during germline calling, pairHMM calculates the likelihood of each haplotype by taking base quality into consideration. My question is: what role does MAPQ play during germline...
View ArticleExit 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 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 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 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.
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