How to run MuTect v1 in Queue?
Hello, I'm trying to set up a queue script that runs MuTect v1 in parallel in scatter/gather mode combined with SGE. I'm using Queue-3.7 and my test script runs in dry-run mode, however when launching...
View Articlehow to split the gvcf file per chromosome?
Hi! My fist post. I have same problem. I have made 60 gVCF file by Haplotypecalle, and then I want to split them per chromosome for the downstream analysis. I used vcftools : command vcftools --vcf...
View ArticleHC listing depth one read less
Hi, I ran haplotypecaller on a bunch of samples using the following commands: java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -drf DuplicateRead -R hg19.fa -I SAMPLE.bam -o SAMPLE.g.vcf -L...
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Error with no Description
Dear GenomeStrip team, My name is Elbay Aliyev. I am working as a Research Specialist at Sidra Medical and Research Center. We have huge project of 3000 Qatari Genome Project and we want to use...
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VariantEval Evaluation Modules Glossary
Table of Contents Default modules: CompOverlap: gives concordance metrics based on the overlap between the evaluation and comparison file CountVariants: counts different types (SNP, insertion, complex,...
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:...
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picard liftovervcf parsing error
I am using picard liftover vcf to algin variants from hg38 to hg19. I am not sure what the error is referring to though it seems to be an issue with the vcf (I have copied a few lines of the format)....
View ArticleHow to reveal why reads are filtered out when using PrintReads?
Hi, when exploring gatk v4.beta.5-36 with PrintReads -I foo.bam -O bar.bam, all my alignments are filtered away: 15:57:37.096 INFO PrintReads - 15201761 read(s) filtered by: WellformedReadFilter Is...
View ArticleComparing variants across samples
Hi, I have called variants from whole transcriptome sequencing data, following the "Calling variants in RNAseq" workflow that you recommended in the Methods and Algorithms webpage and using the...
View ArticleStrange RevertSam error
I recently came across this error using RevertSam, and haven't been able to find forums related to this issue. Any idea what might be causing this? To get help, see...
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Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticlePicard:median target coverage is same for all samples
Hello, I have been redirected by the Picard team to post my query here. I am using Picard HsMetrics to calculate the mean/median coverage for each exon . The baits file is the whole target region of...
View ArticleAnalyzeCovariates fails with error message "RScript exited with 1"
When you run AnalyzeCovariates to analyze your BQSR outputs, you may encounter an error starting with this line: org.broadinstitute.sting.utils.R.RScriptExecutorException: RScript exited with 1. Run...
View ArticleUnsupported major.minor version 52.0
Dear all, first of all I read the other thread about this in this forum: here and the recommended links in that thread. I also found this problem in stackoverflow (here). Unfortunataly I couldn't solve...
View ArticleMuTect2 panel of normals – empty VCF file
Hi, I have successfully run MuTect2 on many paired tumor/normal samples. However, when I try creating a panel of normals (using the the recommended approach), I end up with empty VCF files. Here is the...
View ArticleHard filters for small numbers of exomes
Are there recommended basic hard filters for small scale exome analysis, besides what is provided in Discussion 2806...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
View ArticleConfused about Bootstrapping a set of known sites for Base Recalibration
Dear all, I am working on genomic data from a non-human organism (nematode) for which I do not have a set of known variant sites. The aim of my study is to find the variants within and between 2...
View ArticleMatched normal vs. Virtual Normal
I have a question about the matched normal sample vs virtual normal sample. By definition, a matched normal (MN) is a sample of healthy tissue of the same individual, in order to distinguish germline...
View ArticleBest practice for variant calling on Ion Torrent data with GATK
Hi, I wonder how well GATK works with Ion Torrent data. Is there any recommended practice to handle Ion Torrent data, especially SNP and indel calling, with GATK? Thanks, XZ
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