GATK4's CalculateContamination reports no hom alt sites found
I have been trying to use GATK4's CalculateContamination but the output is not as expected: level contamination error whole_bam 0.0 1.0 The GATK log contained warnings that there was not enough data...
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...
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I got a question about the kmer length you parsed during the second step of...
As I screenshot, I found HC respectively parse the sequence corresponding to the ActiveRegion on reference genome and reads to kmers in length of 10 and 25. Furthermore,...
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Over estimation of AF in Mutect2 (GATK 4.0.2.1) ?
Hi, I ran Mutect2 (GATK 4.0.2.1) followed by FilterMutectCalls with default parameters. I got some passed variants with AF much larger than the alt_depth/total_depth (see attached image), I checked the...
View ArticleMuTect2 LOD calculations
I am interested in how NLOD and TLOD are calculated in MuTect2. The MuTect2.java code...
View Article[GATK4 beta] no filter-passing variants in Mutect2 tumor-only runs using...
Hello, I would like to ask your advice on the tumor only mode of Mutect. I ran GATK4 beta.3's Mutect on 20 tumor samples using tumor-only mode, and found no variant passing filters. Every variant is...
View ArticleFollowing Best practice, I have ERROR:MATE_NOT_FOUND in all my files
I am running Mutect2 on about 100 pairs of tumor-normal samples of whole exome sequencing. I am using GATK4.0.9.0. The pipeline used the recommended best practice pipeline: 1. FastqToSam, 2....
View ArticleHow does a panel of normal affect variant calling using mutect2
Hello, I am running an analyis on tumor samples using mutect2. To investigate the effect of a PON on variant calling , I ran my analysis with and without the PON. Both analyses yield different amounts...
View Articleaccuracy produced by Mutect2 is too low
With simulated data by BAMSurgeon, I tested Mutect2 and Varscan2. There are almost no overlap between Mutect2's vcf and my ground truth while Varscan2's result is resonable. Why? Is my usage is wrong?...
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Mutect2 missed variant called by HaplotypeCaller
Hi, I am running GATK 3.5.0 with java version 1.8.0. I have two cell line samples that I paired with a promega baseline reference (its essentially a mixed germline sample) to run Mutect2 (which I am...
View ArticleOncotator overview and basic usage
Overview Oncotator is a tool for annotating information onto genomic point mutations (SNPs/SNVs) and indels. It is primarily intended to be used on human genome variant callsets and we only provide...
View ArticleEvaluating the evidence for haplotypes and variant alleles (HaplotypeCaller &...
This document details the procedure used by HaplotypeCaller to evaluate the evidence for variant alleles based on candidate haplotypes determined in the previous step for a given ActiveRegion. For more...
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MuTect2 strandbias + TLOD clarification
Hi, I have a set of tumour samples and I would like to call variants using MuTect2 without matching normals, annotate using VEP and filter out known germline variants afterwards. I used tumor-only mode...
View ArticleRun Mutect2 in gatk-4.0.4.0 with an error `java.lang.NumberFormatException:...
Hi there~ When I ran mutect2 in gatk-4.0.4.0,I got something wrong with it. gatk --java-options "-Xmx7g -XX:+UseParallelGC -XX:ParallelGCThreads=8" Mutect2 \ --dont-use-soft-clipped-bases true...
View ArticleMutect2 pipeline fails for some inputs
I'm running a WGS analysis and parallelizing the run for each chromosome. Few chromosomes are failing the somatic variant calling process with the following error. It is really difficult to pinpoint...
View ArticleCurrent status of GATK4 GermlineCNVCaller tools and best practices.
Hi, I would like to try out GATK4 for discovering or genotyping germline CNV's in a cohort of few hundred whole genome sequenced samples. I work with non-human species data, but the genome sizes are...
View ArticleCalculateGenotypePosteriors produces a bunch of zero coverage variants
Hi GATK Team, we are running small targeted panels on GATK4. It seems, most of the Variants (~90%) are DP 0 Variants, emerging after applying CalculateGenotypePosteriors. Before this step we are...
View ArticleInvalid or corrupt jarfile
When I run ./gatk --help it seems to be working fine. However, running anything else such as ./gatk --list produces an error: Error: Invalid or corrupt jarfile...
View Articlesorting a BAM file with PICARD
Dear all, would you please advise: I am using PICARD in order to sort a BAM based on read name (it is a BAM file from EGA that contains cancer sequencing data), and when I do run PICARD SortSam, I am...
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Calling variants in RNAseq
Overview This document describes the details of the GATK Best Practices workflow for SNP and indel calling on RNAseq data. Please note that any command lines are only given as example of how the tools...
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