GATK 3.7 error message: not a strict subset of per read allele map alleles
I am trying to run GATK 3.7 for variant calling and I keep getting this error. Any comments about what this error is? Thanks! ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67): ERROR...
View ArticleSpanning deletion in pooled sequencing studies
Hey GATK team, I have a question regarding spanning deletions in one of my runs. Briefly, the study is set up so that we sequenced 21 pools of 3-5 animals each. Using GATK 3.5, I followed the Best...
View ArticleSVGenotyper walker
1. Introduction The SVGenotyper walker traverses a VCF file to compute genotypes for structural variations. This walker is the main component of the SVGenotyper pipeline. Currently, only genotyping of...
View ArticleWhy "NO_READS" from DiagnoseTargets despite lots of reads in interval?
I a m running DiagnoseTargets on a list of intervals corresponding to targeted exons. In the result file, intervals are filtered by i.e. PASS, LOW_COVERAGE, COVERAGE_GAPS or NO_READS for each sample as...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
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 ArticleRunning genotypeGVCFs with ~4000 human exome data: stuck on "ProgressMeter -...
Hello, I am running genotypeGVCFs with ~4000 human exome data. To speed up the process, I have splited exome.interval_list into sub_interval_list which one interval file contains ~100kb regions. Then I...
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 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 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 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 ArticleDisconcordance between chip run for same sample
Hi all, I am evaluating the panel performance, which was designed based on amplicon enrichment. However, I found that 2 out of 2000 variants showed disconcordance between the two run. For example,...
View ArticleVariantsToVCF Error: Null alleles are not supported
Hi GATK team, I am trying to convert HapMap output files of TASSEL3 to VCF using the GATK VariantsToVCF tool. However, I am getting the error below. I used GATK v3.2-2-gec30cee. Do the "null genotypes"...
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 Articlepositive and negative set in model training by variantRecalibrator
Hello! Thanks for develop this tool set and share with others with good supports, it really contains a lot of wonderful tools. I just try to understand VQSR more into detail. If I give the resources...
View Articlesome questions about difference between HaplotypeCaller and MuTect2
Hi, Recently I have been worked in variant calling using GATK and I have some questions in the process of learning GATK tools. Iām interested in the essential difference between HaplotyepCaller and...
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 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 ./.
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