What is this error?
I'm running IndelRealigner and I got this error , HLA-B13:02:09, HLA-B13:08, HLA-B13:15, HLA-B13:25, HLA-B14:01:01, HLA-B14:02:01, HLA-B14:07N, HLA-B15:01:01:01, HLA-B15:01:01:02N, HLA-B15:01:01:03,...
View ArticleVariantsToVCF Error: Null alleles are not supported
Hi GATK team, I am trying to convert HapMap output files of TASSEL3 to VCF using the GATK VariantsToVCF tool. However, I am getting the error below. I used GATK v3.2-2-gec30cee. Do the "null genotypes"...
View ArticlegenotypeGVCFs vcf files empty, only the header
I'm running genotypeGVCFs on GATK 3.7/3.8, I tried both, but I'm only getting headers on the vcf files. I ran java -XX:ParallelGCThreads=4 -Xmx15g -jar GenomeAnalysisTKjar -T GenotypeGVCFs -R ref.fa -G...
View ArticleWhat is the GATKReport file format?
A GATKReport is simply a text document that contains well-formatted, easy to read representation of some tabular data. Many GATK tools output their results as GATKReports, so it's important to...
View ArticleAbout the coverage file
Is the coverage_file necessary in Mutect analysis? How to get the file? Thanks.
View ArticleError running Picard Tools v2.10.9
Hello- I'm trying to run MarkDuplicates in Picard Tools v2.10.9. Java version is 1.8.0_144. The data is a .bam file that has been sorted and indexed in samtools. (exome capture sequences from HiSeq...
View ArticleIs Indel realignment necessary when HaplotypeCaller re-assembles all reads in...
If HaplotypeCaller re-assembles all reads in a region Why is it recommend to run IndelRealigner first?
View Articlegatk4 Allelic CNV
Hi, I have been using gatk4 alpha for copy number analysis. I have created PoN and did segmentation. Now I want to check for allelic CN which requires heterozygous sites. For now I am using germline...
View ArticleIs there a paper describing the »Haplotype Caller algorithm?
Hi, I'd like to ask you if there is a paper describing the Haplotype Caller algorithm, if you could please send me the reference. I have tried to find it, but I only found the paper on GATK which is...
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 Articlehow to view points distribution and genes across the whole human genome from...
HI, I have a bed file , then I wanna konw how to view points distribution across the whole genome from the bed file ,and also mark genes . my bed format just like this : chr start end...
View ArticleHow to merge genotype info from multiple samples into 1 vcf with only 1...
Hi everyone, How do you at Broad merge genotype info from multiple samples into 1 vcf with only 1 genotype column, because I noticed your resource files used in VariantRecalibrator are formatted this...
View Articlehow to choose sequencing depth for FFPE and cfDNA tumor sample for MuTect2 ?
HI, I am doing target panel sequencing for tumor research . now I have the following questions. for FFPE tumor sample , what's sequencing depth is suifable for M2 calling ？ and for cfDNA tumor sample ?...
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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...
View ArticlePicard IlluminaBaseCallsToSam - clocs file issue - more elements than expected
I am attempting to demultiplex a lane of Illumina HiSeq2500 data using Picard IlluminaBasecallsToSam (v2.5, Java(TM) SE Runtime Environment (build 1.8.0_20-b26)). This tool fails to complete and states...
View ArticleCreatePanelOfNormals problem
I am trying to ues CreatePanelOfNormals for cnv analysis java -Xmx4G -jar /ifshk7/BC_PS/luoshizhi/software/gatk/gatk-4.beta.2-4/build/libs/gatk.jar CreatePanelOfNormals -I...
View Articletag information of SNPs for UG or HC
Hi Is there any way to get the tag information of SNPs for UG or HC? Like in the alignment where you find multiple reads piled up and tag them as different groups. Best, Taslima
View ArticleDoes HaplotypeCaller detect SNPs which are heterozygous (not matching the...
Dear GATK team, I have a simple question regarding the HaplotypeCaller/UnifiedGenotype module. There are 3 options for SNPs in the output depended on the reference. Homozygous for the reference,...
View Article[GATK 4 beta] FilterByOrientationBias for matched normals
In the manual / help-page of CollectSequencingArtifactMetrics, it is said that CollectSequencingArtifactMetrics tool should be run for both the normal sample and the tumor sample, if the matched normal...
View ArticleGATK 3.7 error message: not a strict subset of per read allele map alleles
I am trying to run GATK 3.7 for variant calling and I keep getting this error. Any comments about what this error is? Thanks! ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67): ERROR...
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