GenotypeGVCFs calculateLikelihoodSums NullPointerException
Hi, I run into a NullPointerException exception when trying do use GenotypeGVCFs to merge a set of gVCF files stored via GenomicsDBImport in a database. java.lang.NullPointerException at...
View Articlepicard tool for MarkDuplicates for cram
Hi picarders, I tried to use picard tool's MarkDuplicates to run against cram files, but I failed! Here is the error message: Exception in thread "main" java.lang.IllegalStateException: A valid CRAM...
View Articlesetup local picard against local htsjdk
Hi picarders, Since I am not having success using picard on my cram files, I decided to setup the picard source code along with the htsjdk source code locally, where I put htsjdk (folder with the same...
View ArticlemuTect2: ": Somehow the requested coordinate is not covered by the read. Too...
Hello! I am using muTect2 (in particular I am following this pipeline: http://gatkforums.broadinstitute.org/gatk/discussion/5963/tumor-normal-paired-exome-sequencing-pipeline) but today I am getting...
View Articlehow to set the value "--contamination_fraction_to_filter" of Mutect2 ?
HI, what's the meanning of the Mutect option "--contamination_fraction_to_filter " ? how to set that value ? it's value of ContEst result ？ I know ContEst is used to evaluate the cross-individual...
View ArticleRealignerTargetCreator hangs
Hi GATK team! we have an issue with running the RealignerTargetCreator unfortunately. Commandline looks like this: gatk -T RealignerTargetCreator -R ref.fasta -I /testsample.sorted.bam -nt 32 -o...
View ArticleJoint genotyping exomes is extremely slow (part of the germline...
I am enduring an incredible slow down during my genotyping stage of the haplotypecaller GVCF command series. It is my understanding from the documentation that this step should be rather fast: "This...
View ArticleScatter Gather and Spark together
Hi, I can't find any recommendations on how to use scatter gather and spark together. We do panel diagnosics and whole exomes. Therefore a run may contain up to 60 samples. My first idea was to use...
View Articlepicard markdup error:Value was put into PairInfoMap more than once
Hi, all! I get the error information Value was put into PairInfoMap more than once when I use picard to mark duplication. I have already tested the newest version bwa 0.7.16a and picard 2.10.7. My...
View ArticleDoes GATK work with polypolids?
Hi, I would like to use GATK for SNP variant and indel variant calling in wild relatives of a crop plant. I have a good reference genome for the diploid crop where I could map my reads but my species...
View ArticleHow to edit MULTIPLE read groups in one bam file
Hi everyone, I recently received a WGS bam from Broad for 1 sample, but with about 8 read groups. BSQR kicked it back saying that the sequencer name in the read group is not recognized. Anyways, I need...
View ArticleRunning ASE Read counter on WXS
Hi I wanted to ask if I can use ASE read counter on WXS data, instead of RNA seq. Would it give me the number of times a particular SNP has been observed on the DNA level? And is it correct to...
View ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
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[GATK 4 beta] read_position and clipping filters in FilterMutectCalls
Hello, I would like to understand the clipping and read_position filters better. Is the read_position filter useful because base quality gets worse toward the end of read in Illumina sequencing? And,...
View Articlewhat's difference between a read marked by "sam FLAG 1024" and marked by "...
HI, 1 . when I run the following command : "samtools view -h -f 1024 bwa.raw.bam " , then can not get any reads , so I think BWA do not markduplicates to use" FLAG 1024". 2 after I deal with...
View ArticleJoint genotyping of trio exome
I am running genotypeGVCFs for trio exome datasets (Father, Mother, and Child). java -jar GenomeAnalysisTK.jar \ -T GenotypeGVCFs \ -R reference.fasta \ --variant father.g.vcf \ --variant mother.g.vcf...
View ArticleGATK 4 VariantRecalibrator throws error for missing R path, but only for SNPs
I'm not using the --rscript_file option, but VariantRecalibrator for SNPs still throws an error for it, but it's fine with the exact same command, except -mG 4, in the INDEL run. And it produces the...
View ArticledbSNP_RS seems to not be annotated with Oncotator 1.9.3
Oncotator 1.9 seems to not be annotating dbSNP annotations (dbSNP_RS), leaving all elements blank in this column. Other annotations are correctly annotated. My command line is oncotator -v --db-dir...
View ArticleWhat should I use as known variants/sites for running tool X?
1. Notes on known sites Why are they important? Each tool uses known sites differently, but what is common to all is that they use them to help distinguish true variants from false positives, which is...
View ArticleHaplotypeCaller raises an error with -A BaseCountsBySample
Hi GATK team , FYI I'm getting the following error with GATK 3.7: <br />java -X -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta --validation_strictness LENIENT -I .bam.list \...
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