Tools Documentation Pages are down
Hi, It looks like all the pages for tools documentation are down right now (11:30am EST). See the attached image for the error message I get when I try to visit those pages. ~Daniel Ence
View ArticleDP field seems off after GenotypeGVCFs
Hello, I am merging a large number of gvcfs in batches and everything looks fine except the DP field. In some samples the DP field is not present in the gvcf files (see below) and therefore when...
View ArticleAddorReplaceReadGroup complain about missing Read Group
I have incomplete readgroups in some bam-files, and tried to update them using the recomended script from the tutorial; java -jar $PICARD_JAR AddOrReplaceReadGroups \ I= /work/users/ED-Sam.sorted.bam \...
View ArticleWhy do I get log info in my intervals file?
SO I have been analysis my sequence data and try to do realignment. After I run the cmd RealignerTargetCreator I got the interval files. However the intervals file start with first line as: There were...
View Articlewhat's the difference if do IndelRealigner first,then to bqsr ?
HI, I read the BP,found should do bqsr first ,then do IndelRealigner, I do not know what that will affect ,any big effects to bam results appears ?
View ArticleSpeeding up CatVariants to merge 1000s VCFs
Hi, Following the advice seen elsewhere on the forum I have performed variant calling with whole-genome resequencing data on a per-scaffold basis. Now, I need to merge 30000 or so individual VCFs and I...
View ArticleRealignerTargetCreator htsjdk.tribble.index.IndexFactory.loadIndex exception
I'm getting a tribble loadIndex exception from RealignerTargetCreator. I see this exception has been reported quite a bit, and one cause seems to be out-of-date index file. I deleted the .bai then...
View ArticleGENOTYPE_GIVEN_ALLELES mode not work in GATK4 beta
Hi, guys, I tried to run GGA(GENOTYPE_GIVEN_ALLELES) of GATK4.beta.1, but failed with NullPointerException, I'm sure that my input file and parameter settings are OK, cause I have checked my setting...
View ArticleHow can Mutect2 GATK 4 beta be parallelized?
Hello, I am creating PoN for Mutect2 and following an instruction in the comments of Mutect2.java gatk-launch --javaOptions "-Xmx4g" Mutect2 \ -R ref_fasta.fa \ -I normal1.bam \ -tumor...
View ArticlePlease help me to interpret this line. How come I have this disease?
chr1 53676448 . G A 1495.77 PASS...
View Article--dontUseSoftClippedBases In HaplotypeCaller
Hi GATK team, Does using --dontUseSoftClippedBases option in HC affect SNP/indel calling in anyway? Can you please elaborate a little bit on how enabling this parameter affects variant calling? Thanks,...
View ArticleWhat does "the region in not targeted by the enrichment chip" mean?
does it mean this region is not sequenced? chr1 53668182 . T . . NT END=53675682;NT GT ./. chr1 53675849 . C . . NT END=53675853;NT GT ./.
View ArticleCollectVariantCallingMetrics varies depending on version of b37 DbSNP
Please review the questions I posted at https://gatkforums.broadinstitute.org/gatk/discussion/10041/varianteval-error-message#latest. They appear as "Answered" but are in fact not. Thanks.
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 ArticleAnalyzeCovariates error (R)
Hello I am trying to generate a base recalibration plots using AnalyzeCovariate My command is such java -jar GenomeAnalysisTK.jar \ -T AnalyzeCovariates -R GRCh37-lite.fa \ -before...
View ArticleVariantEval error message
Hi everyone, While running VariantEval on ch3 on of a gvcf file, using the following command: java -Xmx32G -jar /home/d/GenomeAnalysisTK.jar -T VariantEval -R /home/d/Human_Reference/hg19ref.fa -eval...
View Articlehow to download the lasted cosmic vcf file
I want to run Mutect2 with the lasted cosmic file. But I can't find where to download it. I search the Forum, and find others may advise to download cosmic file from...
View ArticleUsing GenomicsDBImport to prepare GVCFs for input to GenotypeGVCFs in GATK4
In GATK4, the GenotypeGVCFs tool can only take a single input, so if you have GVCFs from multiple samples (which is usually the case) you will need to combine them before feeding them to GenotypeGVCFs....
View ArticleOrder of reporting sites by GenotypeGVCFS
Hello, When I genotype a large and diverse cohort I often see an error about too many alleles at one position, which is fine. What puzzles me is why the sites in question are not reported in order,...
View ArticleMuTect2 beta --germline_resource for build h19，af-only-gnomad.vcf
Hi - I'm looking to run MuTect2 beta using the --germline_resource option. However,I cannot find af-only-gnomad.vcf for build h19. How can I find this vcf for hg19?
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