Oncotator -- Variant classification and Secondary variant classification
There are 22 values for Variant classification, and 7 values for Secondary variant classification in Oncotator output. Can any one please tell me what the values mean? Also, can any one please tell me...
View ArticleVariant Recalibrator 0 scoring variants
Hi, We've been experiencing an error with the Variant Recalibrator tool in a number of our runs. The error occurred with versions 3.5 and 3.7, with WGS data that shouldn't break the tool due to an...
View ArticleRADseq data and GATK
Hello! I am pretty new to bioinformatics- mostly just have taken one class. I have been handed some RADseq data and we want to do some SNP variant calling. I am trying to make sure that I use GATK...
View ArticleLogging error when connecting to ftp server
Hello! i am trying to run the following command to download the dbsnp_138.b37.vcf.gz and i get a login erro. following my command and error message. am I making any mistakes or the server is having a...
View ArticlePhasing with HC
Hi I'm currently calling variants using HaplotypeCaller on different subsections of a WGS file (<5Mbp). The number of phased variants that show up are very low. How can I increase the 'yield' of...
View ArticleRemoving * Alleles
Hi, The program I am using for analysis considers * alleles inappropriate for analysis. From my understanding these are spanning deletions, but I am unsure how to properly remove them from my data. Do...
View ArticleGBS data and duplicates marking
Hi, I just read this in the Best Practices guide: "Duplicate marking should NOT be applied to amplicon sequencing data or other data types where reads start and stop at the same positions by design."...
View ArticleERROR MESSAGE: Code exception (see stack trace for error itself)
Hi,GATK term I have set up a bwa + gatk best pratices pipeline for variant calling on WES data (50 samples ). I use the haplotype caller in gvcf mode.When I joint gvcf to vcf with the following...
View ArticleGATK4: status of some Picard/GATK3.7 tools missing from alpha?
What are the plans for the tools available in Picard 2.9.2 or GATK3.7 that are not in GATK4 alpha? Is the plan eventually to port everything to GATK4? Or are some being permanently sent out to pasture?...
View ArticleERROR MESSAGE: Input file must have contiguous chromosomes problem
Hi, I am running VariantFiltration on vcf files produced by GATK's (version 3.5-0-g36282e4 )UnifiedGenotyper in vcf.gz format. I tried to solve the problem many times with different solutions but its...
View ArticleDescription and examples of the steps in the CNV case and CNV PoN creation...
The CNV case and PoN workflows (description and examples) for earlier releases of GATK4. For a newer tutorial using GATK4's v1.0.0.0-alpha1.2.3 release (Version:0288cff-SNAPSHOT from September 2016),...
View Articlemerge samples
Hi I have only 4 samples, but each sample has 23 fastq file. So I gernerate 23 gVCF for each sample by GATK-3.7. Finally, I got VCF file by GenotypeGVCFs. However I found that most of snps in VCF file...
View Articlewhere do I find SamToFastq.jar ? [reproducibility?]
Dear Community, I am from system-administrator side, and totally new in this field about bio-informatic, so excuse my weird question. I am attempting to reproduce results of: Nature Biotechnology 33,...
View ArticleHow does VariantEval's CountVariants option determine MNPs?
Hi, I am trying to understand what CountVariants is calling as an MNP in my dataset. When I run CountVariants, I get ~3K MNPs called across my samples. However, when I run SelectVariants with...
View ArticleDifference in output file from Picard's MarkDuplicates
Hi, I'm working on a pipeline which takes a RNA-seq bam file and looks for overlaps using R. When I run the R script on my original BAM file it works fine, however when I run it on the bam file...
View ArticleUnifiedGenotyper command -o not found
Hello everyone, I am running UnifiedGenotyper, which works, it gets to the very end where it says "DONE" and then no file is generated since it says "-o command not found" I have already tried using an...
View ArticleSNP distribution across chromosome
Hi, I wonder to ask -is there any tool in the GATK to calculate SNPs/Indels distribution in each chromosome based on 100kb or 1 MB window size? Thanks.
View ArticleTrisomy 21 and de novo mutations
I'm looking for de novo mutations in children with Trisomy 21. I have sequence for 4 trios (mother, father, child with Trisomy 21). I have run Haplotype caller with ploidy 2 and with ploidy 3, then...
View ArticleException in thread "main" java.awt.HeadlessException while running...
Running the following command using the latest GATK4 jar file (GenomeAnalysisTk-4_1.jar): java -jar GenomeAnalysisTk-4_1.jar PrintReads -I /home/exampleBAM.bam -O outputBAM.bam At first I had this...
View ArticleBaseRecalibrator: Lexicographically sorted human genome sequence detected in...
Hello, I've tried everything but still get an error: when I run: java -jar /data/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R hg19.fasta -I reordered.bam -knownSites hg19.dbsnp.sorted.vcf -o...
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