Unable to download GATK 3.6
Hello, I am logged in to my account on gatk forums but unable to download GATK 3.6. I get various errors including "Error retrieving content: Could not load requested content from the forum database....
View Articlemills indel hg38
Hi all! I would like to use indelRealigner, but I didn't find Mills indel vcf for hg38. Could anyone give me a link where I can find it? Thank you in advance best
View ArticleGATK License and galaxy
Our lab provides a protected instance of galaxy to our registered users ( N=~24 and growing ) Those users come from anywhere in France. Can I legally wrap GATK into a galaxy tool for our users ?
View ArticleUsing MuTect2 with RNAseq data with a PoN (no matched normal)
Hi ! I am trying to construct a panel of normals since I don't have any matched normal for my tumour sample to run MuTect2. So as I have read in this forum, this PoN should be built with data that has...
View ArticleDepth of Coverage: Only first gene summary output
Hello, I've been trying to run DOC on a sorted RefSeq Gene list downloaded from the UCSC Table Browser as described in the DOC guide doc. After sorting/formatting, only the first record in the ref seq...
View ArticleAsterisk in the alt feild of VCF?
I have output from the GATK pipeline that includes an asterisk "*" in the alternate allele field at some positions in the VCF file. e.g. chr1 801995 . G A,* 9566.82 PASS...
View ArticleVariant annotations at multialleleic sites
I was wondering how variant annotations are calculated for sites with multiple alternate alleles. Annotations like AC and AF have an entry for each allele, but annotations like QD and SOR only have one...
View ArticleSelectVariants --removeUnusedAlternates option not working
Dear GATK team, I am using GATK version 3.2-2 and am trying to process a vcf file with SelectVariants to remove variant calls where the sample is homozygous for the reference allele. I have a joint...
View ArticleQueue with Grid Engine
1. Background Thanks to contributions from the community, Queue contains a job runner compatible with Grid Engine 6.2u5. As of July 2011 this is the currently known list of forked distributions of...
View ArticleMinimising Batch Effects in VariantRecalibration
Hi there, I've checked the best practices and documentation to look for correct way to run VQSR to prevent the dreaded "No data found" error. What keeps popping up is not to run single-sample vcf's but...
View ArticleHaplotype caller in GATK 4, a.k.a the hellbender
I am trying to use GATK 4 to run the tools in a scater/gather fashion using Spark. For example, I was able to run printreads using PrintReadsSpark. However, now I am trying to run the Haplotype caller,...
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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 Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
View ArticleERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the...
Hi, I'm currently working with bwa, samtools and GATK to make SNP calling on Medicago truncatula. I'm using my own reference sequence, with the 8 chromosoms in the same fasta file. C1_lenght=155648...
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Analysis of genome evolution over time with GATK
Dear GATK team, as a first time user of GATK I have a conceptual question that is related to the analysis of my experiment (I have already searched the forum for many hours now and did not find...
View ArticleJoint analysis on germline SNP discovery between paired-samples
Hello, I have a cohort of several sibling pairs, and I am interested in finding Germline SNPs for each pair. Furthermore, I understand from the best practices that a joint analysis using the Haplotype...
View ArticlePicard Output Gives Malformed Bam and other files
I ran Picard with the following script without error, but when I ran GATK after that, I got error message that says the .bam file and .bai files are malformed. java -Xmx25G -Djava.io.tmpdir=tmp -jar...
View ArticleHow to validate sam/bam at every step
If I use Picard tool ValidateSamFile, it is unclear to me know this can make difference. It only gives error report. So, do I have to go into bam/sam to delete those errors manually?
View ArticleHaplotypeCaller - Genotype Given Allele Mode
Hi Team, I want to call variants for some samples using Genotype Given Allele mode(GGA) of HaplotypeCaller. I have used UnifiedGenotyper earlier in GGA mode. I am not sure about the right approach to...
View ArticleCollected FAQs about interval lists
1. What file formats do you support for interval lists? We support three types of interval lists, as mentioned here. Interval lists should preferentially be formatted as Picard-style interval lists,...
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