GenotypeGVCFs: WARNING: of INFO fields not parsing
The HC calls in issue were called in a complete GATK 3.6-0/ JDK 1.8 workflow as follows: java -Xmx64G -jar $GATK_JAR -T HaplotypeCaller -ERC GVCF -R $REFGENOME -I $INPUT_FILE -o...
View Articlepiping GATK output to stdout
I want to pipe GATK output to standard output. I am using a command like this (GATK v2.8-1-g932cd3a): java -Xmx4g -jar GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T CombineVariants -V in1.vcf.gz -V...
View ArticleGATK 4 CNV Proportional Coverage for WGS : Firehose task "ERROR SparkUI:...
Hi - Today I've been trying to use the "GATK 4 CNV Proportional Coverage for WGS " (version 4) task in Firehose copied from Algorithms Commons. After 16 warnings: WARN Utils: Service 'SparkUI' could...
View ArticleWhat input files can I annotate with Oncotator?
Input formats supported by Oncotator VCF -- As seen in the version 4.1 http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 MAFLITE -- maflite, which is a...
View Articlewindow size in haplotypecaller's output bam
Hi, I am using HaplotypeCaller to re-align reads according to a set of pre-existing somatic variant calls. So far, this seems to work well; however, when I review the output bam in IGV, I notice that...
View ArticleClik here to view.
Empty output file and providing malformed VCF file error when using GATK ContEst
Hi all, Recently I have used ContEst for estimating cross-sample contamination.Firstly I downloaded all example data from CGA website http://www.broadinstitute.org/cancer/cga/contest_download and used...
View ArticleHow should I pre-process data from multiplexed sequencing and multi-library...
Our Best Practices pre-processing documentation assumes a simple experimental design in which you have one set of input sequence files (forward/reverse or interleaved FASTQ, or unmapped uBAM) per...
View ArticleGenotyping VCF with HC
Hi, I am using Haplotype Caller to genotype a VCF file. I am using this exact command line: java -Xmx20g -jar GATK/3.6-0-g89b7209/GenomeAnalysisTK.jar \ -T HaplotypeCaller -R $indexFasta -I $Bam -o...
View ArticleFiltering of heterozygotes only
Hi! I need help, please! I'm working on lovebirds and trying to identify SNPs that can be included in a parentage verification panel. The reference genome is the offspring and then I have mapped its...
View ArticleWhy do MQRankSum and ReadPosRankSum not appear in some vcf file entries?
Hi all, I've generated a vcf file of SNPs having used HaplotypeCaller, CombineGVCFs, GenotypeGVCFs and SelectVariants. However, when I try to extract annotations from each line in the vcf, I find I am...
View ArticleGATK 3.6 GenotypeGVCFs Failure: java.util.zip.DataFormatException: invalid...
I am attempting to genotype a set of gVCFs, which I have bgzipped and indexed with tabix. This worked up to the point of receiving the seemingly odd error message: ERROR...
View ArticleContESt for WGS data
I running contEst with silico diluted whole genome sequenced data to detect the contamination levels. The numerical values of predicted contamination is corrected, but the values are constantly off by...
View Articleabout HaplotypeCaller
Dear all, would appreciate an advice please on a simple question : 've been running using HaplotypeCaller -stand_call_conf = 30 (default), while some of our collaborators used -stand_call_conf=20. In...
View ArticleObtaining phased haplotype info for individuals from the 1000 genome project
Hi, I am trying to obtain the phased haplotype of a very specific region of a human gene for 3 individuals that participated in the 1000 genomes project. I used the Data slicer tool to down load the...
View ArticleFurther information about MuTect2 filters (clustered_events,...
Dear GATK developers, We are using MuTect2 for variant calling and we have noticed that several variants fail to pass filters such as clustered_events, homologous_mapping_event, str_contraction and...
View ArticleReversions: an Algorithm issue
Since this is an algorithm question that covers both types of MuTect, I'd rather raise it here. I have noticed the variant calling model in MuTect seems to require AF[TUMOR] > AF[NORMAL] to be...
View Articlehow to build/get populationAlleleFrequencies.vcf for ContEst
How to build/get populationAlleleFrequencies.vcf for ContEst ? and what is the necessary field of VCF file? AF field? MAF field? I found no guide for this. and I tried 1000G vcf file, but it failed...
View ArticleSomatic mutations based on sliced bam
Hi, I would like to retrieve simple somatic mutations (using mutect2) from a bam file. However, I am interested in mutations in specific areas in the DNA only (for example, specific chromosoms). Can I...
View ArticleStrandBiasbySample, FisherStrand Annotation
Hi, I am using GATK version 3.2-2 to analyze miseq data from a human snp panel, aligned to it's "own" reference. I use unifiedgenotyper to call all desired SNPs (ref or non-ref variants) from the panel...
View Articleabout ContEST
Dear Sheila, would appreciate a suggestion on using ContEST: how shall I modify the command line in order to change the "type of population" (from CEU to any other population, or better, to include ALL...
View Article