GenotypeGVCFs: stand_emit_conf not defined
Hi, I got an error from GenotypeGVCF that says the argument stand_emit_conf is not defined, while the documentation of GenotypeGVCF has that option....
View ArticleGenotypeGVCF output
Hi, I am running joint calling with GenotypeGVCF. The output from the program is being put into an "error" file. This file is being filled with gigabytes of lines similar to "WARN 18:38:59,655...
View ArticleCombineGVCF Error: Malformed VCF
Hi, I generated a GVCF per (human 30x whole genome sequencing) sample per chromosome using HaplotypeCaller, then I would like to combine the GVCFs using CombineGVCF. I got the following error for some...
View ArticleVariantRecalibrator - no data found
I just updated to the latest nightly and got the same error: INFO 12:03:16,652 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00258 INFO 12:03:23,474...
View ArticleHow does Picard's MarkDuplicates handle unique molecular barcodes and PCR error?
Hello, I'm interested in using unique molecular barcodes to help distinguish what is PCR error in my samples. My current understanding of how MarkDuplicates chooses a "best-pair" is that it chooses...
View ArticleSelectVariants --excludeIDs
Does the gatk/3.4-46 version (or older) have the option --excludeIDs? I'm trying to use it but it keep giving the ERROR MESSAGE: Argument with name 'excludeIDs' isn't defined. here the code I'm using:...
View ArticlePooled sample parameters to be used for haplotype callers
Hi Everyone, I want to use haplotype caller for detecting snps, but this time I am dealing with pooled samples. Before pooling and doing sequencing on this WGS exp, I want to ask how GATK HAPLOTYPE...
View ArticleInvalid command line: No tribble type was provided on the command line and...
Dear GATK support team, I have created g.vcf files from 2000 samples. Following GATK's best practices, I want to combine them in sets of 200 samples before proceeding with the joint genotyping. When...
View ArticleCatVariants : g.vcf put underneath one another, not mixed
Hi the team, I have probably misunderstood how to make CatVariants working - probably the assumedSorted function that I don't really understand in the help. I used the following command line to merge...
View ArticleHET or HOM in RNA-seq calls with low allele frequency
I'm using the RNA-seq Best Practices pipeline to look at some of my data, and I'm seeing some calls that I'm having difficulty in understanding. An example site looks like this: A G 5178.77 PASS...
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 Articleusage of the contest-reported fraction contamination for MuTect2
Hi, Suppose I obtain from Contest a fraction contamination value. Is there a way when using GenomeAnalysisTK.jar --analysis_type mutect2 where I can pass in the contest-generated value so that it can...
View ArticleGenomeSTRIP CNVDiscoveryPipeline without LSF
Hello, I am running GenomeSTRIP CNVDiscoveryPipeline on a set of bam files on a server that does not have LSF installed. Is there a separate mode that works on a standalone server, or is LSF a strict...
View ArticleCalculate duplication levels using Picard HsMetrics
Hi everyone, We are using BWA-mem to mark duplicates in our BAM files (using samblaster). We then run Picard HS-metrics to evaluation duplicate levels and other stats...
View ArticleAnother stack trace error while running VariantRecalibrator (SNP mode)
Dear GATK team I just got the attached stack trace error when running VariantRecalibrator in SNP mode. I have tried with and without -nt option. Find also attached the command line I used. Thanks a lot...
View ArticleBase Recalibration plots:RScript exited with 1
I want to create plots before and after Recalibration, and getting the error below: I have checked for the package "ggplot2"which is required for generating graphs and also added the path of R script...
View ArticlePossible to run Variant Recalibration on GVCF
Hi, Should it be possible to run the VariantRecalibrator directly on a set of GVCF files without performing the GenotypeGVCF step (i.e; can I already start Variant Recalibration step 1, while the...
View ArticleHow to force MuTect2 genotype all sites within intervals?
I cannot generate genotypes for all input sites with MuTect2 (-L input.vcf). I tried --output_mode EMIT_ALL_SITES and -gt_mode GENOTYPE_GIVEN_ALLELES without luck. Is there an equivalent option to...
View ArticleMutect2 suggestion - option to output normal sites too
I'd like to see an option for Mutect2 that would allow input of a germline .vcf call file, and output to include all sites present in that file. The --output_mode option could be expanded to include an...
View Article(howto) Install and run Oncotator for the first time
1. Download the Oncotator package, the default datasources package, and (recommended) transcript override list from the Downloads page Please note: Broadies who wish to run the installed Oncotator on...
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