What's in the resource bundle and how can I get it?
NOTE: we are currently working on overhauling the bundle to 1) add support for Hg38 and 2) document the provenance of the resource files more fully. 1. Obtaining the bundle We provide these files (or...
View ArticleBQSR for WES data generated by different exome-capture platforms
Hi everyone, We have over thousand WES samples generated by two different exome-capture platforms. Samples were multiplexed and sequenced on Illumina HiSeq, with each lane containing 3-10 samples....
View ArticleI am getting this error in VariantFiltration --genotypeFilterExpression
$java -jar $gatk -T VariantFiltration -R /storage/sandesh/TargetSpot/genome/Corca1_AssemblyScaffolds.fa -o snpsDP10.vcf --variant snps.vcf --genotypeFilterExpression "DP < 9" --genotypeFilterName...
View ArticleCreating an ubuntu snap package for gatk
I would like to create an ubuntu snap package (snapcraft.io) for gatk, to make it easy for myself and others to install and run gatk like any other program. However, the licence forbids re-distribution...
View ArticleNo varaint calling with Wgsim simulated reads
I have generated 1 million 600bp single ended reads using Wgsim read simulator from chr21 of hg19. All the bases have 40 base quality. The reads are aligned with BWA-MEM and then sorted and...
View ArticleFastaAlternateReferenceMaker to consensus sequence?
How do I create a consensus seq with this command? By default, it fill the gaps with Reference seq but I don't want it, that's not a consensus sequence. I need the gaps be filled by Ns. How to do it?...
View ArticleGoing public with pipeline scripts
Folks, it really makes my day when I get to announce some good news that has been cooking for a long time. So this is going to be a very happy Humpday indeed. The good news (which I may have hinted at...
View ArticleFix chromosome namings in...
Hi, I would say this is my fault but would you mind bring in sync your file in the hg38 bundle on your FTP server? java -jar GATK/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -T BaseRecalibrator...
View Articleproblem with RnaSeqMetrics in Picard CollectMultipleMetrics
When I try to run CollectMultipleMetrics with PROGRAM=RnaSeqMetrics and I= R= O= set to something I get : Exception in thread "main" java.lang.NullPointerException at...
View ArticleCorrect understanding of BQSR
Hi, I just wanted to reach clarification on some issues related to BQSR. We work on bacterial genomes, with approximately 8000 in the collection and about 120 new every week. We asked ourself if BQSR...
View ArticleIs there any way to deal with the absence of an actual reference genome ?
Hi everyone, I am just discovering GATK, therefore I strongly apologize in advance, as my question may sound a bit naive or missing the point ! I am currently working on RAD-seq data obtain from pools...
View ArticleHaplotype caller BP_RESOLUTION :More AD values than alleles called for
My intention is to find different bases called in a particular chromosome location irrespective of it being assigned as SNP/badbase. I user the below command: java -jar 3.5/GenomeAnalysisTK.jar -T...
View ArticleHapmap raw variant to VCF conversion?
Hi I would like to obtain snps+genotypes in .vcf format for a number of lymphoblastoid cell lines, part of the hapmap project. Some of them have been sequenced by the 1000genomes project (so I have...
View Article(howto) Run the genotype refinement workflow
Overview This tutorial describes step-by-step instruction for applying the Genotype Refinement workflow (described in this method article) to your data. Step 1: Derive posterior probabilities of...
View ArticleUsing depth of coverage metrics for variant evaluation
Overview This document describes the proper use of metrics associated with depth of coverage for the purpose of evaluating variants. The metrics involved are the following: DepthPerAlleleBySample (AD):...
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(How to) Mark duplicates with MarkDuplicates or MarkDuplicatesWithMateCigar
This tutorial updates Tutorial#2799. Here we discuss two tools, MarkDuplicates and MarkDuplicatesWithMateCigar, that flag duplicates. We provide example data and example commands for you to follow...
View ArticleError while running HC on ChrX
Dear GATK, I have a set of 4 bam files that I was able to generate genotypes from using HaplotypeCaller for Chr20. I took the same data and tried to call genotypes for ChrX, and received the following...
View ArticleExtracting variants for multiple read groups with VariantsToTable
I have a VCF file representing several related individuals and I want to extract the information into a table using VariantsToTable. All I really need is the genotype for each individual in the set at...
View ArticleVery long run-time - GATK HaplotypeCaller GVCF with Ion proton reads
I analyzing the proton reads using GATK Haplotypecaller. but I have an very long run-time to analyze this data with below command. gatk -Xmx48g -Djava.io.tmpdir=./ -T HaplotypeCaller -nct 8 -R...
View Articlewhole genome versus whole exome PON
Quick question: Do you recommend using a PON made of whole exome samples, if the cancer dataset is whole exome, and similarly use a PON made of whole genome samples, if the cancer dataset is whole...
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