QD Annotation error in GATK in VariantRecalibration step
hi all, i downloaded a BAM file from 1000 genomes to work on and converted it to FASTQ and aligned with bwa mem to hg38, this worked fine. later I wanted to run VariantRecalibration and use the...
View Articlepicard ./gradlew test error
I have an error when tried to run ./gradle tests on my system. I am running Linux Mint 18 system. Could you please let me know what should I do? Thank you. $ java -version openjdk version "1.8.0_151"...
View ArticleGATK4 Realign around indels
Hi, Looking through GATK4 best practices for pre-processing fastq files and do not see a "realign around indels" ( in GATK3 : java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator ) . Should I use...
View ArticleCan't copy GATK tool web page URLs from browser and paste them
If I copy the URL from the Safari browser address box in OSX while the browser is on your web page for RealignerTargetCreator, and then paste the URL back in, the browser gets a Not Found error, and...
View ArticleGenotyping known variants with GenotypeGVCFs
Hi Geraldine, Sheila, and others, Now that it seems that a fix for the "GGA" feature in HaplotypeCaller may be forthcoming in some future GATK release, I was wondering about the prospects for a...
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Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencer when it estimates the quality score of each base...
View ArticleMuTect2 to compare 2 tumor samples
I have capture data of 2 tumor biopsies from 1 patient, and would like to compare the two for mutational similarities and differences. I don't have a normal control. I tested if MuTect2 (4.0.1.2) could...
View ArticlelibVectorLoglessPairHMM is not present in GATK 3.8 - HaplotypeCaller is...
We are running GATK on a multi-core Intel Xeon that does not have AVX. We have just upgraded from running 3.4-46 to running 3.8, and HaplotypeCaller runs much more slowly. I noticed that our logs used...
View ArticleGATK License and Redistributing in an AWS AMI
I have been asked to reach out to you to clarify the GATK license. We are hoping to package our CNV/SNP calling and annotation pipeline that includes GATK and make it available on an Amazon Machine...
View ArticleGenomeSTRiP v2.0 CNV calling
Hi Bob, I upgraded to version 2 and ran my samples with a 30 background population samples from 1000G for DEL discovery. I know that SVToolkit now calls deletions and copy number variation, my question...
View ArticleHow can I attend/host a GATK workshop?
The list of upcoming workshops is available in the Events calendar. You can subscribe to the gatk-workshop mailing list if you would like to be notified of upcoming workshops by email. The course...
View ArticleInstructions for GATK workshops
Preparing for the workshop To follow these instructions and attend the workshop, you will need to have a basic understanding of the meaning of the following words and command-line operations. If you...
View Articleerror when convert human snp138.txt to .vcf format
I have used the following command $ java -jar GenomeAnalysisTK.jar -T VariantsToVCF -V:OLDDBSNP snp138.txt -R genome.fa -o snp138.vcf to convert human snp138.txt file downloaded from...
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(How to) Call somatic copy number variants using GATK4 CNV
This demonstrative tutorial provides instructions and example data to detect somatic copy number variation (CNV) using a panel of normals (PoN). The workflow is optimized for Illumina short-read whole...
View ArticleGetBayesianHetCoverage exits with code 247
When I run GetBayesianHetCoverage in a Docker container, the function exits without completing with code 247. The Docker container is built from an image that uses the Debian "Stretch" base image, with...
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 ArticleRecommendation Interval length for genomicsdb import
Dear GATK Team Is there any recommendations for the length of one interval specified in genomicsdb import? I am running a genomicsdb import for about 50 bam samples (from cattles) for whole length of...
View ArticleVariantAnnotator is not annotating variants with InbreedingCoeff
Hi, I am using GATK VariantAnnotator to annotate my VCF with the InbreedingCoeff but when I check the output VCF I see that no variant was annotated with the InbreedingCoeff. I've used a pedigree file...
View ArticleMuTect2 Discards lots of reads?
MuTect2 discards 74.26% of the reads as below, becasue of 39% duplicate reads ans 34 % notprimary reads.Below is Star alignments we have higher mapping? And below is my commad, I don't have matched...
View ArticleUnable to load library 'lsf': liblsf.so and Unable to load library 'drmaa':...
I am running CNVDiscoveryPipeline and it is throwing following error Unable to load library 'lsf': liblsf.so. The command used is java -Xmx150g -cp ${classpath}...
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