CollectRnaSeqMetrics - RIBOSOMAL_BASES
Hi, I am having a problem with RIBOSOMAL_BASES estimated as 0. When I open the mapped reads I observe several reads at ribosomal positions. The same problem is discussed in another forum but no...
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DP in the VCF is different from the number of reads in the bam file after...
I have called SNPs and want to use the reads number. However, I found in the VCF file the DP is A(which will be shown in the attached file). However, in the bam file which is used for SNP calling using...
View Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
View ArticleGATK and MuTect licensing moves to direct-through-Broad model
We have some important news to share with you regarding the licensing of GATK and MuTect. The licensing agreement between us and Appistry will end effective April 15, 2015; from that point on, the...
View ArticleASHG 2016 in Vancouver - Terrible weather, exciting science!
The weather in Vancouver is awful right now, and that's probably a good thing -- it should keep the outdoorsy types like myself from succumbing to the natural beauty of British Columbia and skipping...
View ArticlemuTect2: ": Somehow the requested coordinate is not covered by the read. Too...
Hello! I am using muTect2 (in particular I am following this pipeline: http://gatkforums.broadinstitute.org/gatk/discussion/5963/tumor-normal-paired-exome-sequencing-pipeline) but today I am getting...
View ArticleBug in HaplotypeCaller: Lines meant to STDERR go to STDOUT
I use HaplotypeCaller v. 3.6-0-g89b7209. I want to compress the output before writing it to the disk and use command like this: gatk -T HaplotypeCaller ... -o /dev/stdout | grep -v -e --- -e WARN |...
View ArticleRunning out of memory
Hello, I wanted to check how can I handle Running out of memory issues when I execute any GATK command? Regards, Satish
View ArticleMQ0Fraction, HWP, Dels Tags for VCF file (How to generate)
Hi, My issue might be very fundamental. I am looking for the values for the tags mentioned in the title after running variantAnnotator on the VCF file. However, they were mentioned in the header...
View ArticleIs CreateSequenceDictionary.jar still available?
Hi When I use MergeBamAlignment, I encountered the following error message. No sequence dictionary found for /home/delta/./ref/hg19_tmp/chr1.fa. Use CreateSequenceDictionary.jar to create a sequence...
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(How to) Map reads to a reference with alternate contigs like GRCh38
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section. This exploratory tutorial provides instructions and example data to map short reads to a reference...
View ArticleHow to get GenotypeGVCFs to not emit sites with no data
Hello, I am working with RADseq data and the vast majority of my reference genome thus has no data for any individual. But when I run GenotypeGVCFs, I am getting a huge VCF file because a missing data...
View ArticleTimeout acquiring a lock - caused by GC pauses
I am trying to run GenotypeGVCFs over a couple of hundred whole genomes. Besides the fact that it uses obscene amounts of RAM, I noticed that it was failing with the message: ERROR MESSAGE: Timeout of...
View ArticleRecommended protocol for bootstrapping HaplotypeCaller and BaseRecalibrator...
I am identifying new sequence variants/genotypes from RNA-Seq data. The species I am working with is not well studied, and there are no available datasets of reliable SNP and INDEL variants. For...
View ArticleFinish Running Svreprocess and Svdiscovery no result in xxxx.discovery.vcf.gz
When I finished Svreprocess, I check the output in xxxx.discovery.vcf.gz,there is nothing under the header ##fileformat=VCFv4.2 ##ALT=<ID=DEL,Description="Deletion">...
View ArticleCan't get calls for multiple records at same position in the alleles input...
Is there a way in the UnifiedGenotyper using the GENOTYPE_GIVEN_ALLELES mode to generate an output vcf line for each of multiple records at the same position in the vcf alleles input file? Thanks
View Articlepicard 2.6.0 ValidateSamFile produces an exception for BGZF file with invalid...
Hi, I ran out of disk space while running our mapping pipeline. When running picard's ValidateSamFile tool on one of the bam files, it produced the Exception below. I'm not sure this is a bug per se,...
View ArticleHashMap iterator problem with GATK 3.6 on NA12878 validations
Hi all; I was running validations with the latest GATK 3.6-0 release and ran into an issue on NA12878 where a region around the centromere on X fails with a HashMap NoSuchElementException. I tried to...
View ArticleWhat is the best way to make an in-house database with allele frequency (like...
Hi, I am currently working on making a pilot in-house database of around 35 exomes data we have in our laboratory. I am following the GATK best practices guidelines for data analysis. The following...
View ArticleTwo validated variants missed by HaplotypeCaller using MIP data (amplicon...
Dear GATK, We are using MIPs (amplicon like) data to analyze the variants for certain genes. However, in two independent samples two validated variants were missed by the HaplotypeCaller. We were...
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