Cannot connect to ftp server
Hey there:) I cannot access the ftp server. I tried the following using filezilla: Host:ftp.broadinstitute.org Protocol: ftp User: anonymous Password: I get these errors Error: The data connection...
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Wrong results with QD,bug?
@valentin @Geraldine_VdAuwera Hello, I do HaplotypeCaller twice，then compared the result vcf files with notepad++ plugin Compare.I found some different value about the QD annotation: java -Xmx12G -jar...
View ArticleNullPointerException in PhaseByTransmission
Hi all, Has anyone else gotten the following: java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(PhaseByTransmission.java:242) at...
View ArticleSegment Mean must be finite
I ran GATK4 AllelicCNV program and get an error message saying "Segment Mean must be finite." (see below) I look at the input files I give the program and no values were listed as "Inf" or "Infinity"...
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 ArticleFile is not a supported reference file type
I am following a tutorial for variant analysis and to create sequence dictionary they have written following command: java -jar ~/bin/picard-tools-1.8.5/CreateSequenceDictionary.jar \...
View ArticleHow to call somatic mutation if I have only tumor sample when exome sequencing
Hello, some tumor samples from FFPE are absent from normal control, we performed exome sequencing. In this situation, how to detect somatic mutation?
View ArticleSingle-Sample Genotyping: Different Workflow?
Hi, If I need to independently call and genotype a single sample, is there a different workflow or set of GATK tools and settings that I ought to use instead of using haplotypecaller to generate a GVCF...
View ArticleDoes GATK 4 support multiple bam files as input?
In the command line help message, it says --input,-I:String BAM/SAM/CRAM file containing reads This argument must be specified at least once. However, if we actually give multiple input files, it says...
View ArticleGenotypeGVCFs AD=0
Hi! I have a sample for which HaplotypeCaller identifies the following variant: chr12 133237753 . GAAA G,GA,GAA,TAAA,GAAAA,GAAAAA,<NON_REF> 66.73 ....
View ArticleStack Trace, number format exception error
Hi, I have a number of bam files that I have downloaded from TCGA, for a number of them I keep getting the following error, both with mutect1 and mutect2 in GATK v3.7: Any help would much appreciated....
View ArticleDetection of competitive spike-ins
We've developed a method for estimating the 95% confidence intervals for MAF (Blomquist 2015) using amplicon NGS libraries. We'd like to extend this into bait capture and whole genome libraries. The...
View ArticleDuplicate Key Error in GATK4 Haplotype Caller
Hello, I have been trying to resolve an issue that occurred in some of my samples while running GATK4 Haplotype Caller. After the program has been running for a while, it suddenly stops and this error...
View Articlev3.7-0-gcfedb67: -T RealignerTargetCreator does not support --known blah.vcf.gz
Hi, it seems GATK does not relaize that it has opened a vcf.gz (actually vcf.bgz file). java -Djavaio.tmpdir=. -jar /scratch/mmokrejs/GATK/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T...
View ArticleRealignerTargetCreator: vcf or vcf.gz?
Dear all I have generated Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi with tabix when running RealignerTargetCreator should indicate the tbi file among the inputs? is it correct to us use...
View ArticleCombineGVCFs includes header from dbsnp file?
Dear GATK team, I have encountered some strange behaviour when running CombineGVCFs (version 3.7-0). When I include a dbsnp file with the -D flag, it appears the entire header of this file is included...
View ArticlePicard SortVcf fail for no reason ?
Hello, Command line(s) you ran: java -jar picard.jar SortVcf I=cosmic/cosmic.vcf O=cosmic/cosmic.srt.vcf SD=reference/GRCh38.d1.vd1.dict Program console output and metrics files. Repetitive console...
View ArticleProblem with running Mutect2 and CosmicCodingMuts.vcf
Hi I have project on tumor and normal samples I have trouble in running mutect2. I found I should do sorting step by Picard SortVcf but I got another error. Please take a brief look at my pipeline and...
View ArticleNo output file from Picard's MarkDuplicates
Hi, I'm working on a pipeline which takes a BAM file and produces a layout file for viewing in software the team uses. I'm working on unix command line and have Java/1.8.0_60 installed. I've integrated...
View ArticleP_GERMLINE output parameter in Mutect2, GATK4
Good Afternoon, I am running a Beta version of GATK4 (installed early this week, I assume it is the latest) MuTect2 tool. I noticed it does not report "SOMATIC" any more, instead it reports some...
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