Variant calling using a phased genome as reference
Hello, I want to do variant calling in a diploid organism using a phased genome as a reference. Therefore, in the reference we have both chromosomes represented. For variant calling with Haplotype...
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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 ArticleWhy does FastaAlternateReferenceMaker output a fasta sequence that is shorter...
Hi everyone, For all GATK commands described below, I am running GATK v3.5. Having called and filtered SNPs and Indels across 312 samples (using Haplotype Caller, Combine gVCFs, Genotype gVCFs, Select...
View ArticleSuggestions for WGS 5X Sequences
Hi Geraldine or Sheila, I am in the process of customizing a GATK pipeline for processing aDNAA. I have processed a couple of 3000 year old WGS sequences so far using GATK best practices, and although...
View ArticleCOSMIC and dbSNP files for MuTect
I'm having trouble finding the recommended COSMIC and dbSNP file for hg19 to use with MuTect (hg19_cosmic_v54_120711.vcf and dbsnp_132_b37.leftAligned.vcf). I can't find these in any of the bundles on...
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Which datasets should I use for reviewing or benchmarking purposes?
This article is out of date and has been archived. We will post a new article replacing this one when we publish new benchmarks for the GATK4 release. New WGS and WEx CEU trio BAM files We have...
View ArticleGATK 3.8 log4j error
I just upgraded from GATK 3.7 to the newly released GATK 3.8 (3.8-0-ge9d806836) and I am getting a StatusLogger error: ERROR StatusLogger Unable to create class...
View ArticleMuTect source now available in GitHub!
Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to...
View ArticleQuestion about Picard ReorderSam: New reference sequence does not contain a...
Hi Picard team, I encountered a problem when trying to reorder downloaded bam files (mapped to hg38) according to my own hg38 reference. There are many contigs that are unique to either fa reference or...
View ArticleError: Unable to retrieve result, with "VariantRecalibrator"
My command lines are as following: java -Xmx8g -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R $GenomeReference \ -input $InputVCF \ -nt 6 \...
View ArticleWhat is purpuse of multiple True Sites in VQSR
I have 3 questions: 1- What is the exact purpose of having both HapMap and Omni True Sites in VQSR, vs just one; 2- If I want to restrict the variant calling to my custom list of positions. Which of...
View ArticleReduce verbosity of cromwell run
Is there a way to reduce the verbosity of cromwell run? It prints a lot of information, in very long lines, which makes it difficult to see where exactly things went wrong if a workflow fails. I...
View ArticleHC listing depth one read less
Hi, I ran haplotypecaller on a bunch of samples using the following commands: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -drf DuplicateRead -R hg19.fa -I SAMPLE.bam -o SAMPLE.g.vcf -L...
View ArticleMulti threading in GATK 4 is done with spark now?
In GATK4 noticed I can't use -nt or -nct with tools that support it in GATK 3.x, and I understand that you removed it due to the complexities that it introduced to the code from this discussion:...
View ArticleGenotypeGVCFs sample specific genotype columns
Hi, I have generated 9 .g.vcf files from my .bam files, and want to do joint genotype calling with all these gvcf files using GenotypeGVCFs tool. I have the following command: java -jar...
View ArticleCalculateTargetCoverage error
Hello, Sorry - I'm very inexperienced at this. I'm trying to follow this documentation: https://gatkforums.broadinstitute.org/gatk/discussion/9143 I was a little unclear on what to use as the target...
View Articlepicard downsampling cram files failed!
Dear GATK, I am trying to conduct downsampling on our cram file. However, the run failed! Here is the command line I used: java -Xmx16G -jar /software/picard.jar DownsampleSam I=H2NCHCCXY-7.hgv.cram...
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[GATK 4 beta] clustered_events in Mutect2/FilterMutectCalls
Hi, I have a question about filtering Mutect2 calls. A well-characterized SNV (vcf records below 17:7577120) is filtered out by clustered_events filter. It appears that an artificial haplotype is...
View ArticleSelectVariants - Exclude variants shared with a certain genotype
Hi all, I'm using a non-model organism to call variants on some UV generated mutants. The reference genome is not perfect, so I sequenced WT along side my mutants. I'm now to my final, filtered .vcf...
View ArticleHow can I get a common variant of three samples from multi-sample VCF after...
Hi. Iām studying about sequencing data analysis followed GATK Best practices for Germline SNP & Indel Discovery. Through the series of analysis, finally I get multi-sample VCF file from joint...
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