Regarding 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 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 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 ArticleAllele Depth (AD) is lower than expected
The problem: You're trying to evaluate the support for a particular call, but the numbers in the DP (total depth) and AD (allele depth) fields aren't making any sense. For example, the sum of all 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 ArticleHaplotype caller
Hi, The version of GATK i have installed is unable to find command "HaplotypeCaller", i have the following versions of GATK installed. version 2.0-0-gb142977 (built from git) version 2.0-0-g4c0ffd4...
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...
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