Problem with joint genotyping
Dear Team, I am running joint calling (according to Best Practices). I have ~800 samples from 3 different centres.First I run CombineGVCFs on cases from batch1(~130samples), controls from...
View Article--cosmic option for Mutect2 in GATK 4.0 beta version?
Hi, What is the current option for "--cosmic" in Mutect2 tool name under GATK 4.0 beta version? I am trying to call variants in a panel of unmatched normals. Thank you.
View ArticleGetBayesianHetCoverage exits with code 247
When I run GetBayesianHetCoverage in a Docker container, the function exits without completing with code 247. The Docker container is built from an image that uses the Debian "Stretch" base image, with...
View ArticleIntervals and interval lists
Many of our workflow recommendations and example commands involve intervals or lists of intervals, which you can specify in your command line using -L (or -XL to exclude specific intervals). So where...
View Article[ERROR] CreatePanelOfNormals
I am trying to use CreatePanelOfNormals for build a PoN. java -Xmx128g -Djava.library.path=/usr/lib/jni/ -jar /root/gatk-protected.jar CreatePanelOfNormals -I...
View ArticleHow to fix the error Unable to access jarfile GenomeAnalysisTK.jar
I have been trying to open the GATK and I always get the same error message: Unable to access jarfile GenomeAnalysisTK.jar. I have a Mac with OS X Yosemite. I also have the latest version of java...
View ArticleSpark in other clusters?
After experiencing some issues with GATK 3.2 on CentOS 7.4 (AVX changes broke everything), we've installed the newer versions - 3.8. I thought I'd install 4 beta to test, but am confused by all this...
View Articlehow does gatk haplotypecaller work in calling SNP with multiple threads?
hi,everyone! I am working on a project where i need to find variant sites(single Nucleotide variant),and i want to accerlerate it with multiple threads,I would like to know how to modify my code(C++)...
View ArticleCombining RAW_MQ and MQ
Hi, I have two batches of gvcfs : - one was processed using GATK-3.3 - one was processed using GATK-3.5 I want to perform a joint calling + VQSR using both batches together. The problem is that the...
View ArticleWhy is HaplotypeCaller spending 8 hrs on "Strictness is SILENT" step?
Hi, I am running HaplotypeCaller on whole genome re-sequenced (~10X coverage) African buffalo genomes, using a high coverage African buffalo genome as the reference (~90X). The genome is about 2.8Gb....
View ArticlePicard: refFlat file not accepted
Hi there, I'm having some issues getting Picard to work. I want to run the CollectRnaSeqMetrics function, but it requires the input of a refFlat file. I'm having some trouble getting this refFlat file...
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Can't run any GATK4 tools on GCS dataproc
I'm having a strange issue running GATK4 tools on a dataproc cluster. I'm submitting from a Broad VM with an empty bash profile. As an example, here's what happens when I try to reproduce this...
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Understanding and adapting the generic hard-filtering recommendations
This document aims to provide insight into the logic of the generic hard-filtering recommendations that we provide as a substitute for VQSR. Hopefully it will also serve as a guide for adapting these...
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(How to) Map and clean up short read sequence data efficiently
If you are interested in emulating the methods used by the Broad Genomics Platform to pre-process your short read sequencing data, you have landed on the right page. The parsimonious operating...
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热烈欢迎我们的中国朋友 / A warm welcome to our Chinese friends
科研圈的亲们，我们来啦！携手国内重量级公司和机构，我们这次给大家带来了高效、规模化使用GATK的技巧！ Today we are reaching out to the Chinese research community with great news: we are partnering with key companies and institutions in China to...
View ArticleGATK v3.8 install
hello,I install the GATK 3.8,and then give me it : # tar: Ignoring unknown extended header keyword LIBARCHIVE.creationtime' tar: Ignoring unknown extended header keyword SCHILY.dev' tar: Ignoring...
View ArticleGenotypeGVCFs variant IDs
Hi there, I am trying to use GenotypeGVCFs to perform joint genotyping on 16 samples. These 16 samples were sequenced twice on two different machines, so I actually have 32 readsets. I called variants...
View Articleobsolete index parameters
Hello, We have a bunch of gVCFs created with an older version, when the flags -variant_index_type LINEAR -variant_index_parameter 128000 --filter_mismatching_base_and_quals were still necessary for...
View ArticleGATK4 MuTect2 passing germline events?
Dear GATK team, I have been experimenting with calling somatic variants in my tumor/normal WES data using GATK4 MuTect2. After calling and filtering, I found many sites (mostly indels and MNP indels)...
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(How to) Generate an unmapped BAM from FASTQ or aligned BAM
Here we outline how to generate an unmapped BAM (uBAM) from either a FASTQ or aligned BAM file. We use Picard's FastqToSam to convert a FASTQ (Option A) or Picard's RevertSam to convert an aligned BAM...
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