Can GATK 4 output all reference sites after joint genotyping?
Hi GATK, My question is if its possible to run --includeNonVariantSites in GATK 4? Ari
View ArticleAllele balance filtering
I am getting a number of incorrect/questionable genotype calls after proceeding through the "Best Practices" guidelines. These incorrect calls are resulting in a lot of false positives in my subsequent...
View ArticleVariantFiltration Request
Does GATK have a tool, probably an extension of VariantFiltration that I'm not seeing, that replaces variants within an interval with Ns on a per sample basis? My idea is the same as an interval list,...
View ArticleCan GATK4.beta3 detect CNVs in whole exome sequencing?
Can GATK4.beta3 detect CNVs in whole exome sequencing?
View ArticleLeft Align and Trim variants aligns 0 variants and results in an empty VCF
I have split the MAVs from exac vcf into individual lines and now pushing it through LeftAlignandTrimVariants walker. the output VCF is empty. INFO 18:45:26,188 HelpFormatter -...
View Articleerror_Values for InbreedingCoeff annotation not detected for ANY training...
Hi, when I run VariantRecalibrator using the following commands: run_gatk.sh -T VariantRecalibrator -R GRCh37/human_g1k_v37.fasta -input raw4.snp.vcf...
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question about ‘gatk4beta’
When I used 'gatk4beta', nothing was produced. Maybe it stoped while running 'grep -i avx /proc/cpuinfo'. I can't avoid this problem, no matter what module I used. My command: 1)java...
View ArticleGATK 3.8 logger ERROR
Hi, after updating to GATK 3.8 I found the following ERROR in my log file. ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:f...
View Articlerunning gatk snp call in KNL computing node (Intel Xeon Phi 7250)
Hi there, I would like to run gatk SNP call in TACC stampede2 machine (https://portal.tacc.utexas.edu/user-guides/stampede2) and they have the KNL node equipped with Intel Xeon Phi 7250. This CPU is...
View ArticleConverting FASTQ to BAM
I'm trying to convert FASTQ to BAM file using FastqToSam and I'm using the following syntax: java -jar Downloads/picard.jar FastqToSam \ FASTQ=Path/filename.fastq.gz \ OUTPUT=Path/filename.bam \...
View ArticleGenome STRIP SVPreprocess error
Hi I'm running genomestrip and I got this error I'm testing whole human genome to find out SVs with Genome STRiP. I used bwa, picard with Homo_sapiens_assembly38.fasta (GATK bundle) Here's my command...
View Articletrio pipeline
Dear friends I am analyzing a trio I have followed the pipeline described in van der Auwera et al. 2013 on each person individually up to HaplotypeCaller and VariantRecalibrator is there a pipeline I...
View Articlesmall .bam files to test GATK Variant Discovery pipeline
Could someone refer me to where I could download the smallest possible .bam files to test my GATK Best Practices Variant Discovery pipeline? My pipeline uses the -L option to parallelize over different...
View Article(howto) Install software for GATK workshops
Objective Install all software packages required to attend a GATK workshop. Prerequisites To follow these instructions, you will need to have a basic understanding of the meaning of the following words...
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 ArticlePedigree / PED files
A pedigree is a structured description of the familial relationships between samples. Some GATK tools are capable of incorporating pedigree information in the analysis they perform if provided in the...
View ArticleWhich training sets / arguments should I use for running VQSR?
This document describes the resource datasets and arguments that we recommend for use in the two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration), based on...
View ArticleSNV gets dbSNP annotation in one sample, doesn't get annotated in another one
Hello everyone, I recently run HaplotypeCaller for GATK3.7 on a series of samples (several GATK runs performed at the same time), using the latest release of dbSNP(150). This was the command line I...
View ArticleRegardign the GENCODE annotation files
For my analysis I want to use GENODE Grch 37 fasta and annotations. For the annotation during the variant calibration and apply calibration; for the resource option where do I get the VCF files. I...
View ArticleHow to build a Mutect Filtering PoN
Hi, Does anyone have a sense of Mutect Filtering PoN, like "final_summed_tokens.hist.bin". I want to try to build one. But, I don't know how. Thank you very much! I will really appreciate your help....
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