Issue with GATK Best Practices for Germline SNP & Indel Discovery in Whole...
The links on the GATK Best Practices for Germline SNP & Indel Discovery in Whole Genome and Exome Sequencepage and corresponding pages appear to be broken/not functioning. website:...
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 ArticleError in genotypegvcfs
Hi I am running GenotypeGVCs and got the following error: ERROR stack trace java.lang.NullPointerException at java.util.LinkedList$ListItr.next(LinkedList.java:893) at...
View ArticleFiltering vcf on per sample AD and PL
Hello, I would like to filter my multi-sample vcf using per sample metrics such as AD and PL. However, these are provided as comma-separated lists of numbers. Does anyone know how I can filter, for...
View ArticleWhat do GATK workshops cover?
This is the description of our current 3-day workshop formula. 3-Day workshop summary This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit,...
View ArticleSelectVariant from FILTER column
Hi, Dear GATK Team I am wondering is there any option in GATK'S SelectVariants walker (I am quite sure that its the best as per my need) to select all those variants which have 'SnpCluster' record in...
View ArticleVariant Filter error
Hello, I am running the Variant Filter command as follows java -Xmx40g -jar GenomeAnalysisTK.jar -T VariantFiltration \ -R g1k.fasta \ -V merged_samples_recalSNPs.vcf \ -G_filter "GQ < 30.0 || DP...
View ArticleGetting Error , Kindly Help
Command : java -jar gatk -T IndelRealigner -R refGenome.fa -targetIntervals sample1_sortedPos_rmdup_addRG_realn_targets.list -I sample1_sortedPos_rmdup_addRG.bam -o...
View ArticleDo checks for Mendelian violations via -ped require both parents to be...
Hello, I am interested in checking my VCF for Mendelian violations using the -ped engine option and the -mv -invMv options of SelectVariants. To see how it works, I simulated SNP genotypes for a...
View ArticleASECounter vs AD and DP in vcf file
Dear GATK developer: Can you please explain the difference between the allele counts obtained by running ASECounter and the allele read counts provided in the AD/DP fields in vcf file. It seems that...
View Articleminor improvement to the VariantsToBinaryPed doc page
On the VariantsToBinaryPed doc page here, the link to PLINK should be updated to this, I think. Moreover, the sentence "the first 6 lines" should be updated to "the first 6 columns", no? Best, Tim
View Articleambiguous explanation of -invMv for SelectVariants
Hello, on the SelectVariants doc page (here), it is written that the following command: java -jar GenomeAnalysisTK.jar \ -T SelectVariants \ -R reference.fasta \ -V input.vcf \ -ped family.ped \ -mv...
View ArticleLot of Missing information GATK
Hello, I have tried using GATK Haplotyper caller. Something, that I noticed is lot of missing genotype calls. Below is the screen shot. Could you suggest if I need to include anything in my parameters...
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Understanding and adapting the generic hard-filtering recommendations
This document aims to provide insight into the logic of the generic hard-filtering recommendations that we provide as a substitute for VQSR. Hopefully it will also serve as a guide for adapting these...
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 ArticleASEReadCounter
Hi, I am trying to use "ASEReadCounter" and have one question regarding "--sitesvcf" option. For vcf file, I used the individual data and got only several lines as results (less than I expected). I...
View ArticleWhat is uBAM and why is it better than FASTQ for storing unmapped sequence data?
Most sequencing providers generate FASTQ files with the raw unmapped read sequences, so that is the most common form in which the data is input into the mapping step of the pre-processing pipeline....
View ArticleAlignment and Variant calling using hg38DH
Dear GATK Team, I want to perform alignment and variant analysis for whole genome sample using hg38DH build. I have gone through forum and came to know that it is quite different. here is the reference...
View ArticleWhy did I get an empty vcf file after using GATK's indel caller?
This is the code: java -jar /Users/RyanYeo/Desktop/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -R /Users/RyanYeo/Desktop/hg38Patch7.fa -T UnifiedGenotyper -I...
View Articlequery about VQSR
Hi, I am using VQSR for non human species, I have the below error message. ((ERROR MESSAGE: Invalid command line: No training set found! Please provide sets of known polymorphic loci marked with the...
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