How does gatk deal with bam XA tag when calling variations?
Hello, When a read has mutli-hits on a reference genome, the bam file would record mutli positions in XA tag. So, would GATK consider the XA tag when calling variations? After getting filtered VCF...
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A dog, a ship and an algorithm that measures relatedness
What is beagle. Beagle is a type of dog known for its even temper and intelligence. It is also the name given to the ship Darwin sailed to the Galapagos (the H.M.S. Beagle), where he developed his...
View ArticleVQSR Runtime error - Version v3.7-0-gcfedb67
Hi, we are getting the following runtime error while processing a SNPs only Whole Exome VCF file with four samples and approx 90,000 variants. Searching the forum we found other people had reported the...
View ArticlePicard FilterSamReads not working
Hello, I am using FilterSamReads in Picard to remove reads from a BAM file that are 1) marked as either both first/second of pair and 2) do not have a mate pair. I am supplying the program with a .txt...
View ArticleSome questions about the results of CalculateGenotypePosteriors
Hi, First, I want to know why when the AD of my data is 0,18 ,it converts the Genotypes from 1/1 to 0/1? (for example: GT:AB:AD:DP:GQ:PL:PP 0/1:.:0,18:20:5:309,21,0:265,0,5. The site number in vcf file...
View ArticleComparing variants across samples
Hi, I have called variants from whole transcriptome sequencing data, following the "Calling variants in RNAseq" workflow that you recommended in the Methods and Algorithms webpage and using the...
View ArticleGATK got "Cannot run program "Rscript": error=5, Input/output error"
Hi, TEAM I use the AnalyzeCovariates of GATK but I got some error information about Rscript. my code is following: /hwfssz1/ST_HEALTH/Population_Genomics/User/dangningxin/bin/java/jre1.8.0_144/bin/java...
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Haplotype Caller: too many alternative alleles found?
Hello gatk team, I am running HaplotypeCaller on 5 files of genomic alignments together at once. Despite the fact that I did a InDel realignment (Indel Realigner gatk) before running these files with...
View ArticleReverse select interval list
I have a file with RNA editing sites which I want to remove from my VCF. I can select all the RNA editing sites with: java GenomeAnalysisTK.jar \ -T SelectVariants \ -R human_g1k_v37.fasta \ -V...
View Article"TOKENS_PON" is for WGS?
Hi, I want to analyze somation mutations in my own WGS data using Firecloud. I am a little bit confused about the ”TOKENS_PON” (as shown in the following) for Mutect filter. Based on...
View Article(howto) Recalibrate variant quality scores = run VQSR
Objective Recalibrate variant quality scores and produce a callset filtered for the desired levels of sensitivity and specificity. Prerequisites TBD Caveats This document provides a typical usage...
View ArticleGATK 4 and deploying GATK in Hadoop Spark environments
Hello GATK Team, I am trying to identify what genomics tools can be deployed in Hadoop Spark environments. I must confess my list is short, I believe GATK is the closest to reach this capability. Can...
View Articlemutect-1.1.7 stack error
I was looking at this post because it appeared to have the same problem that I am having http://gatkforums.broadinstitute.org/gatk/discussion/6054/stack-error-when-run-mutect-the-first-time ; however,...
View ArticleVariantsToBinaryPed java.lang.ArrayIndexOutOfBoundsException: -1
Hello, can you please help me sort out the following error in running VariantsToBinaryPed: java -jar /sb/project/fkr-592-aa/data/GalWaRat/bin/third/gatk-3.7/GenomeAnalysisTK.jar -T VariantsToBinaryPed...
View ArticleGATK4 beta Mutect2 misses --cosmic option
could anyone explain why the --cosmic option is removed? Also, should --germline_resource be used with --dbsnp or replace it? Thanks!
View ArticleAC and AF Allele frequency field are giving two values in the VCF File
Hello team GATK, I have finished generating VCF files by following GATK best Practices documentation. And for some positions the AC and AF field have two values (Mostly Repetitive). Is it normal? If...
View ArticleCombining variants from different files into one
Solutions for combining variant callsets depending on purpose There are three main reasons why you might want to combine variants from different files into one, and the tool to use depends on what you...
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Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
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Malformed walker argument
Hello, I installed GATK package as explained in the documentation, but I am not able to use the "walkers" with go with it. I always this error message: java -jar GenomeAnalysisTK.jar -T IndelRealigner...
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