ERROR: GATK VQSR fails to identify top worst variants and terminates
Hi, I've been using GATK's VQSR to my satisfaction in multiple projects, however, today have encountered the same failure on multiple seemingly normal exomes. Here's the log. INFO 16:01:37,398...
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(How to) Run the GATK4 Docker locally and take a look inside
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section. 1. Install Docker on your...
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9 Takeaways to help you get started with GRCh38
We are starting official support of GRCh38, a reference genome with alternate contigs. In fact, going forward all of our new projects will use GRCh38. During this transition over the coming year, we...
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(howto) Perform local realignment around indels
This tutorial replaces Tutorial#2800 and applies to data types within the scope of the GATK Best Practices variant discovery workflow. We provide example data and example commands for performing local...
View ArticleVariantRecalibrator returning empty result files
Hi, I'm running the VariantRecalibrator step on a pretty small data set (50 samples in the cohort, but only for Chr21 from a whole exome sequencing project), and GATK is returning empty result files...
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(howto) Discover variants with GATK - A GATK Workshop Tutorial
GATK TUTORIAL :: Variant Discovery :: Worksheet June 2016 - GATK 3.6 This tutorial covers material taught at GATK workshops, and focuses on key steps of the GATK Best Practices for Germline SNP and...
View ArticleHC step 4: Assigning per-sample genotypes
This document describes the procedure used by HaplotypeCaller to assign genotypes to individual samples based on the allele likelihoods calculated in the previous step. For more context information on...
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Mutect2 not detecting variant visible in tumor and matched cell line bam
I am unable to detect a particular variant when running Mutect2 on a tumor and tumor-derived cell line exome data. I ran each with the corresponding matched normal. The image below displays, from top...
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how to choosing a java training institute according to best learning and I am in Chennai suggest me the best java training institute in Chennai
View ArticlePicard AddOrReplaceReadgroups
Hi all, I'm getting an error "ERROR: Option 'RGID' cannot be specified more than once." The command I use is: picard -jar /path/to/picard.jar AddOrReplaceReadGroups I=/path/to/bam.bam...
View Articlepicard 'failed to uncompress the chunk' error
Hi, I have the jobs failing seemingly randomly using picard v2.12.1 LiftoverVcf tool with an error 'failed to uncompress the chunk' . The error stack: Exception in thread "main"...
View Article[ERROR] token_pon_size_update
I ran “token_pon_size_update” two times to build a PoN using hundreds of TCGA blood samples. But, each of them finally failed because of a file transfer issue. Should I try to run the tasks separately?...
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What are the parameters used by GATK to define a SNP?
I'm a master student and I'm using GATK, for the first time, to find SNP in RNAseq data. I would like to know what GATK considers a SNP. What are the parameters used for this, such as: frequency and...
View Articleit seems that since GATK3.7, info fields from parent VCFs are not kept the...
Hello there, I used to run the following command, to merge VCF from 2 callers (freebayes et GATK); infos fields were first preceded by a unique tag, both in the headers and in each record, to be sure...
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QD Distribution for sequence capture data
Hi there, I am working with sequence capture data from a non model organism (based on a de novo genome). Our goal is to get the site frequency spectrum for use in demographic inference, so the number...
View ArticleToolName for ReadLengthFilter
Hello! I am trying to use ReadLengthFilter to remove the reads shorter than a certain length threshold. According to the online documentation, I used the following command: java -jar...
View ArticleHow do other samples support the genotyping of one sample in a multisample...
Hi, I would like ask how is the data of other samples used to support the genotyping of one sample in a multisample case (GenotypeGVCFs)? I see very low AD values (relative to the other allele ADs and...
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BSQR removing variants
Greetings, I have exome data of two siblings. I followed the best practices haplotypecaller gvcf instructions and encountered a weird situation. Reference genome hg19 is used in analysis. There is a...
View ArticleConverting FASTQ to BAM
I'm trying to convert FASTQ to BAM file using FastqToSam and I'm using the following syntax: java -jar Downloads/picard.jar FastqToSam \ FASTQ=Path/filename.fastq.gz \ OUTPUT=Path/filename.bam \...
View ArticleHighly different number of SNPs between Unifiedgenotyper and Haplotypecaller...
I ran two different SNP callers to compare my data but they showed highly different numbers of SNPs. for Unifiedgenotyper java -Xmx48g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -drf DuplicateRead...
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