Using GenomeStrip to genotype known vcf
Hi, I want to genotype known CNVs (from 1000G Phase3, GoNL, etc.) in our samples using GenomeStrip without performing any discovery step at first. 1) Do I have to run only the SVPreprocess steps...
View ArticleThe error of the genomestrip's Svpreprocess
Hi,I'm just use the genomestrip to call the sv from pigs. I have 30 bams and then follow the introduction to prepare the reference file ,genomeMaskFile ,copyNumberMaskFile and ploidyMapFile files.But...
View ArticleVersion highlights for GATK version 3.8
One more 3.x version, for the road! That's right, even as we're ramping up our efforts on GATK4 (we're three beta releases in at this point, and getting down to brass tacks writing the migration guide...
View ArticleVQSR and VariantAnnotator on Samtools VCFs
Hi everyone! My goal is to run VQSR on VCFs generated with samtools mpileup. According to GATK best practices first i have to run VariantAnnotator on each of my VCFs in order to do that. here's the...
View Articlefailed on the pipeline of BamToUnmappedRGBams_MC
I jut got this error: message: Job BamToUnmappedRGBamsWf.ValidateSamFile:0:1 exited with return code 3 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute...
View ArticleGATK events update for Fall 2017: ASHG and more!
Fall is my favorite season -- it combines the best weather in New England and the most active period of the year for GATK events and announcements (although sometimes the latter means we don't get to...
View ArticleMuTect2 Pitfalls
I was looking for information about MuTect2's accuracy and found a pitfalls summary on Read the Docs. Some of the examples are alarming. Will these issues be fixed in an upcoming version?
View ArticleGRCh37/hg19: should I re-process my BAMs?
I have a human exome experiment on which I am using hg19 resources (reference, targets, dbSNP, ... the whole shebang). I want to add some 1000Genomes exomes to this experiment, but the available BAMs...
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...
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View ArticleWhole Genome Sequencing data analysis
Hello, We are new in whole genome sequencing (WGS) data analysis. Earlier received lots of help and suggestions from GATK team regarding whole exome sequencing analysis and in-house database...
View ArticleImplementation of SOR
Hi, I found that SOR implementation is not something that is stated here. final double ratio = (t00 / t01) * (t11 / t10) + (t01 / t00) * (t10 / t11) The above means that R + R in the documentation,...
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...
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View ArticleUnifiedGenotyper removed samples?
Hello everyone. I'm using GATK to call SNPs on data set of 54 samples, however, after I used UnifiedGenotyper I noticed that my vcf file now contains 24 samples, so 30 samples were removed. I used dcov...
View ArticleGATK 3.7 and GATK 4 beta2
Dear team, I am using GATK 4 Beta2 for testing HaplotypeCaller for our NGS workflow. The command which I used is: time -p /gpfs/software/genomics/GATK/4b.2/gatk/gatk-launch HaplotypeCaller \...
View ArticleIn haplotype variant caller for the Influenza virus, do I need to mention or...
I have sequenced influenza virus and interested in finding variants (SNVs and INDELs). I am planning to use Haplotype caller.
View ArticlePossible inconsistency in GATK 4.beta.6 source code
Hi GATK Team, We are porting GATK4 to run on GPUs. We have found an inconsistency in the behavior of GATK 4.beta.6 in clipRead() functionality in ReadClipper.java while using HaplotypeCaller. If the...
View ArticleIf I run mutect2, do I still need to run Indelocator?
Hi, I wonder if Indelocator will provide extra indel variants that mutect2 could not call. Thanks, Bo
View ArticleOncotator question
hi,I have some confusion about oncotator。 I use this tools to annotate vcf in order to get variation information，but this file size is too large because use all annotation database，can we select...
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