IllegalArgumentException: samples cannot be empty
I am trying to run HaplotypeCaller on some data that I know is messy and would fail some of the filters, so I have run it both with and without --disableToolDefaultReadFilters. Either way I don't get...
View ArticleTruth or control samples - Variant calling
Are we able to incorporate truth/control samples in addition to dbSNP when calling variants with GVCF (cohorts) or the traditional way with HaplotypeCaller. There are for example situations where the...
View ArticleUsing JEXL to apply hard filters or select variants based on annotation values
1. JEXL in a nutshell JEXL stands for Java EXpression Language. It's not a part of the GATK as such; it's a software library that can be used by Java-based programs like the GATK. It can be used for...
View ArticleProblems running ExtractIlluminaBarcodes and/or IlluminaBasecallsToSam
I've been trying to use picard tools to demultiplex directly from Illumina base calls to unmapped bam files, with no success. I have a slightly unusual setup with dual (sample) barcodes on the reads,...
View ArticleIlluminaBasecallsToSam Fails, trying to figure out why
Hello, I ran ExtractIlluminaBarcodes and came out with the following metrics file: METRICS CLASS picard.illumina.ExtractIlluminaBarcodes$BarcodeMetric BARCODE BARCODE_NAME LIBRARY_NAME READS PF_READS...
View ArticleUnifiedGenotyper miss some alleles while using GENOTYPE_GIVEN_ALLELES mode
Dear GATK team, We are using UnifiedGenotyper GENOTYPE_GIVEN_ALLELES modes to do genotyping, but we found that not all given alleles were genotyped. For example, the input vcf is: 13 20763485 . AG A 30...
View Articlegetting HaplotypeCaller to work
Hi all, I am new to WGS analysis. I have paired end reads, so I used 'bwa mem' to get the .sam file and then samtools to create the .bam. Next the sorting and marking duplicates has been done with...
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Parallelism
This document explains the concepts involved and how they are applied within the GATK (and Crom+WDL or Queue where applicable). For specific configuration recommendations, see the companion document on...
View ArticleMuTect2 beta --germline_resource for build b37
Hi - I'm looking to run MuTect2 beta using the --germline_resource option. However, I've consistently used the b37 genome build throughout my analaysis, while the suggested resource (gnomad) appears to...
View ArticleBase Recalibration
Hi I am not much familiar with bioinformatics and SNP Genotyping. As I am trying to identify the SNP in my sample from SRA Database so this the pipeline i am following I - STAR Aligner to mapping II -...
View ArticleGenotype Called by HaplotypeCaller
Hello, I'm running GATK pipeline for Variant calling. First starting with...
View ArticleGATK workshop (Oxford)
Hi! GATK team, I remember there is a workshop in Oxford (9/18~9/20). Is it cancelled? Thanks! Dada
View ArticleScatter Gather and Spark together
Hi, I can't find any recommendations on how to use scatter gather and spark together. We do panel diagnosics and whole exomes. Therefore a run may contain up to 60 samples. My first idea was to use...
View ArticleTool documentation
Where has the tool documentation gone to? I keep getting 404 errors when trying to follow links to specific tools (from google) or the general tool documentation area.
View ArticleRegarding Gatk output
Hello, I want to identify snps in my sequencing data.I am new in this field so i am just following guideline that you provided. i have paired end sequencing data (one sample) and according to...
View ArticleTools Documentation Pages are down
Hi, It looks like all the pages for tools documentation are down right now (11:30am EST). See the attached image for the error message I get when I try to visit those pages. ~Daniel Ence
View Article#CHROM characters allowed
Hello, I am trying to use GENOTYPE_GIVEN_ALLELES through HaplotypeCaller and have never run into this problem before. Everything is running as I expect, however I am really not getting any results even...
View ArticlePicard LiftOverVcf produces duplicate positions
Hi, I have produced a set of VCF files with UnifiedGenotyper, using a custom BED file. Subsequently I have used Picard LiftOverVcf in order to lift these VCF files from hg38 to hg19....
View ArticleDP field seems off after GenotypeGVCFs
Hello, I am merging a large number of gvcfs in batches and everything looks fine except the DP field. In some samples the DP field is not present in the gvcf files (see below) and therefore when...
View ArticleAddorReplaceReadGroup complain about missing Read Group
I have incomplete readgroups in some bam-files, and tried to update them using the recomended script from the tutorial; java -jar $PICARD_JAR AddOrReplaceReadGroups \ I= /work/users/ED-Sam.sorted.bam \...
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