picard markdup error:Value was put into PairInfoMap more than once
Hi, all! I get the error information Value was put into PairInfoMap more than once when I use picard to mark duplication. I have already tested the newest version bwa 0.7.16a and picard 2.10.7. My...
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 ArticleTCGA legacy archive, muTect v119?
Hello, I want to reproduce some of the .vcf files I got from TCGA legacy archive from their .bam files. The headers included the following line:...
View ArticleRunning genotypeGVCFs with ~4000 human exome data: stuck on "ProgressMeter -...
Hello, I am running genotypeGVCFs with ~4000 human exome data. To speed up the process, I have splited exome.interval_list into sub_interval_list which one interval file contains ~100kb regions. Then I...
View ArticleRunning GATK from docker repository on Cancer Genomic Cloud (CGC)
Hello! I'm having some problems running GATK on the Cancer Genomic Cloud (CGC) platform. I've created my own tool using the following docker repository ''' broadinstitute/gatk:4.beta.5 ''' I'm using...
View ArticleHaving Facebook Password Reset Problems ??? Then not to worry solve it step...
Regardless of every such service offered, Facebook Support Number gives various tech support and services. Despite the fact that user can get different arrangements, yet our group is best in giving the...
View ArticleFacebook Expert Help and Support
There is an obvious number of online networking stages accessible, the most used is certainly Facebook. With a specific end goal to appreciate the applications, administrations, and highlights,...
View ArticleRealignerTargetCreator hangs
Hi GATK team! we have an issue with running the RealignerTargetCreator unfortunately. Commandline looks like this: gatk -T RealignerTargetCreator -R ref.fasta -I /testsample.sorted.bam -nt 32 -o...
View ArticleGenotypeGVCFs 3.8 fails
I had the same problem as described in thread 10004: ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in Except my issue was with...
View ArticleHow to use HaplotypeCaller for paired samples?
I have paired disease-normal data sets for each sample. If I want to call SNPs and in-dels using HaplotypeCaller, how should I proceed?
View ArticleMuTect2 beta --germline_resource for build b37
Hi - I'm looking to run MuTect2 beta using the --germline_resource option. However, I've consistently used the b37 genome build throughout my analaysis, while the suggested resource (gnomad) appears to...
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MuTect2 beta --germline_resource file
Hi, I'm new in using MuTect2 I'm a bit confused that the gnomAD file provided on gnomad.broadinstitute.org/downloads is about three times larger than the gnomAD file provided on...
View ArticleCromewell 28: Root Configuration Not Working ?
Hello, I have edited my cromwell configuration to use a custom location for where the workflow executions should go. See the line: root: "/btl/store/dev_cromwell_executions" In this configuration file:...
View ArticleBaserecalibrator warn : index dictionary utils
Hi! Everyone! I have a question. I have analysed 60 WGS files, and used GRCh38 reference genome from broadinstitute. I have been doing Baserecalibration using dbsnp_146.hg38.vcf.gz and...
View ArticleAn error in the GATK4 GetPileupSummaries
Hi, I have been trying to follow the steps outlines by this tutorial https://drive.google.com/drive/folders/0BzI1CyccGsZicXl0anMwQnFYVEU. Everything worked fine but then I got stuck at the...
View ArticleMay I use CleanSam by default?
I'm thinking about implementing CleanSam into the NGS analysis pipeline after alignment. Will it be OK to run CleanSam and only after that run ValidateSamFile to be sure that files are ready for...
View ArticleWhy is gatk4 GetPileupSummaries always failed ?
I used the following command /home/projects/cu_10098/apps/src/gatk-4.beta.5/gatk-launch --javaOptions "-Xmx20g" GetPileupSummaries \ -R /home/databases/gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta...
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(howto) Discover variants with GATK - A GATK Workshop Tutorial
GATK TUTORIAL :: Variant Discovery :: Worksheet June 2016 - GATK 3.6 This tutorial covers material taught at GATK workshops, and focuses on key steps of the GATK Best Practices for Germline SNP and...
View ArticleWhat are the differences in using default and custom interval list (-L) for...
I mean to say default interval list (-L) as exome region and custom interval list as designed and given by the company like agilent or illumina. What will the difference in the output generated using...
View ArticleWhy is Inbreeding Coefficient not always displayed in a vcf file?
Hi there, Using GATK v3.5-0, I've generated vcf files for a group of 223 whole genomes, one per interval of the reference genome. I created GVCF files using Haplotype Caller in 'GVCF' mode, before...
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