gatk4.beta.2 :IndexFeatureFile problem
I am trying to ues IndexFeatureFile to reindex a vcf gatk-launch IndexFeatureFile -F redo.vcf however,that command exits with this message: A USER ERROR has occurred: The IndexFeatureFile tool is...
View ArticleSomatic Variant Calling with Tumor Samples Only
Hi, I recently went to the workshop for variant calling and mentioned that I would like to perform somatic variant calling with Mutect using only tumor samples (no matched normal sample). I was told...
View ArticleBiallelic variants only with HaplotypeCaller
I want to restrict the HaplotypeCaller to only call biallelic sites. I'm thinking that this can be accomplished with --max_alternate_alleles, although I'm not 100% whether this parameter should be set...
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...
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DP differences between haploid and diploid mode
I would appreciate some help in understanding better the differences between haploid and diploid mode when it comes to calling and joint-genotyping (HaplotypeCaller + GenotypeGVCFs) in gatk. In...
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 ArticleGATK v4 Variant Recalibrator command line
Could someone please provide me with a sample command line to run Variant Recalibrator for GATK v4? I am running the tool using GATK 4 Alpha with the following command line:...
View ArticleIs my RNAseq experimental design suitable for SNP calling?
Hello fellows, I am a newbie here and would highly appreciate your advice about one particular experimental design. We have data from RNAseq experiment which was originally designed to assess...
View ArticleVersion highlights for GATK version 3.8
One more 3.x version, for the road! That's right, even as we're ramping up our efforts on GATK4 (we're three beta releases in at this point, and getting down to brass tacks writing the migration guide...
View ArticleMultiallelic indel with HaplotypeCaller-GenotypeGivenAlleles
I'm seeing unusual behavior when trying to force genotyping of a polymorphic repeat expansion/contraction variant - rs34983651. The reference sequence starting here is CATATATATATATATAA... and the...
View ArticleSplit'N'Trim Errors
Hello all, I am having a problem during the Split'N'Trim phase of the RNAseq Best Practices. The script I have used is as follows: java -jar /data1/APPS/gatk/GenomeAnalysisTK.jar -T SplitNCigarReads \...
View ArticleAlternate Reference Maker
When I run the command: java -jar '/home/bushra/Downloads/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar' -T FastaAlternateReferenceMaker -R '/home/bushra/Downloads/Brassica/Bra1.27.fa' -o...
View ArticleGenotypeGVCFs not working for 4.beta.3
I am using GATK beta 4.3 (downloaded yesterday) on trio whole-exome data, following best practices on germline SNP/indel calling up to HaplotypeCaller. I was unable to follow the example command in...
View Articleit's a bug for the calculation of Mutect2 allele frequency ?
HI, when I used Mutect2 to call mutations . I got this bug , chr3 12649448 . C CCAAA GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:139,66:0.143:0:1:.:138,31:0:5 . 66/(139+66) = 0.32, not...
View ArticleMultithreaded HaplotypeCaller gives different GVCF files to single-core run
Hi, I've been recreating a bioinformatics pipeline for paired WGS data which largely follows the GATK best practices, but I'm having issues with HaplotypeCaller to create a GVCF file for one...
View ArticleSnpEff html and .vcf file result are not matching
Asslamu Alikum I have successfully managed to run SnpEff for my vcf files. However, the count of missense variants in my html file and the VCF file generated by SnpEff are different. Missense in HTML:...
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 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 Article[GATK4 beta] no filter-passing variants in Mutect2 tumor-only runs using...
Hello, I would like to ask your advice on the tumor only mode of Mutect. I ran GATK4 beta.3's Mutect on 20 tumor samples using tumor-only mode, and found no variant passing filters. Every variant is...
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Variant Quality Score Recalibration (VQSR)
This document describes what Variant Quality Score Recalibration (VQSR) is designed to do, and outlines how it works under the hood. The first section is a high-level overview aimed at non-specialists....
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