Enable multithreading in genomeSTRiP
Hi Is there a way in genomeSTRiP to enable specify the number of threads the program can utilize? I've got a 56-core server and would like to maximize my usage of the available resources for...
View ArticleFiltering multi-sample VCFs for low DP
Hi Team, I have a multi-sample VCF file produced by UnifiedGenotyper. I now want to filter this file marking those variants with a low depth. However the DP entry in the info field is across all...
View ArticleCollectRnaSeqMetrics - no coding reads found
Hello, This is my code: java -jar picard-2.8.0.jar CollectRnaSeqMetrics \ I= bam/Aligned.sortedByCoord.out.bam \ O= output.RNA_Metrics \ REF_FLAT= bam/refFlat.txt \ STRAND=NONE \ RIBOSOMAL_INTERVALS=...
View Article[GATK4 beta] no filter-passing variants in Mutect2 tumor-only runs using...
Hello, I would like to ask your advice on the tumor only mode of Mutect. I ran GATK4 beta.3's Mutect on 20 tumor samples using tumor-only mode, and found no variant passing filters. Every variant is...
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Can I use GATK on non-diploid organisms?
In general most GATK tools don't care about ploidy. The major exception is, of course, at the variant calling step: the variant callers need to know what ploidy is assumed for a given sample in order...
View ArticleCan ASEReadCounter take indels?
Can ASEReadCounter calculate allele-specific count correctly on indels? I've seen some old posts about a bug for this (https://gatkforums.broadinstitute.org/gatk/discussion/6723). I wonder if it was...
View ArticleGenotypeConcordance
Hi, I have the following problem: I am evaluating genotype concordance using: -T VariantEval --evalModule GenotypeConcordance -comp ref.vcf -eval sample1.observed.vcf If I use a reference genotype file...
View ArticleGATK4 SplitNCigarReads RuntimeIOException: Attempt to add record to closed...
On a Linux cluster, I ran this command on a node (no job scheduler): ./gatk SplitNCigarReads -R /bigdisk/databases/genomes/human/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa -I 28_tumor.dedupped.bam...
View ArticleMutect2 outputting samples with AD of "."
I've setup a workflow that runs Mutect2, which completes successfully, but the AD of all variants is output as "." This is an issue as we use the AD for downstream stages. Is there any reason this...
View ArticleCombineVariants Key . found in VariantContext field INFO but this key isn't...
I have encountered the following error when trying to merge two VCFs from different callers: Key . found in VariantContext field INFO at chrM:711 but this key isn't defined in the VCFHeader. We require...
View ArticleRegarding of piping - Picard and BWA (Align and MergeBamAlignment step)
I made 3 bam files with **command in below.** Picard version: 2.17.8 BWA version: 0.7.17-r1188 compression_level=2 java_opt="-Xmx32G" bwa_version="0.7.17-r1188" bwa_commandline="mem -K 100000000 -p -v...
View ArticleGATK v4.0.1.1 HaplotypeCaller
I am using GATK v4.0.1.1 HaplotypeCaller for variant analysis. (paired-end DNA sequenced data mapped to the reference using BWA mem). The command I used; “gatk HaplotypeCaller –R Reference.fna –I...
View ArticleGenotype qualities/Qual scores for All sites
Hi I am trying analyze 8 exome datasets. In the final output, I want to get calibrated QUAL or Genotype scores for each position (even if it is homozygous ref) in the target region. I am following the...
View ArticleWhere to download Normal exome bam for creating PoN for cancer CNV workflow
Hi, We are trying to get the copy number variation of the tumor only samples (from bam files) using the below workflow (not having paired normal samples)...
View ArticleHow can I access the documents/articles found in a post?
When I tried to click on an article/document linked in the "HaplotypeCaller in a nutshell" post, it gave me the following message: Error retrieving content: Could not load requested content from the...
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Error in GatherBQSRReports
Hi, starting from WES pair-end data... in the BaseRecalibrator step I used as interval these regions/chr: chr1-22, chrX, chrY, chrM, alternative contings and HLA contings. In the case of HLAname I...
View Articlegatk 3.4-46-gbc02625 runtime error with RealignerTargerCreator
Hi, I'm sorry if this is a repeat question. I have been searching through old questions and have yet to find an answer which has fixed the issue. Thank you for your time! I am trying to create...
View ArticleDetection of somatic mutations with RNAseq - Mutect2
Hello, We are working on a swine model of melanoma, where tumors trigger an efficient immune response, most likely by producing neoantigens, ie proteins carrying somatic mutations and thereby...
View ArticleInformation regarding the GATK Workshop in Taiwan
Hi, a colleague and I are quite interested in doing a GATK 4 training. Today I've seen the announcement in the event calendar that there is one of your larger trainings coming up in March in Taiwan. To...
View ArticleGermline VQSR recommended settings
Hi, we've been looking at the new Best Practices pages and at the WDLs linked there. In particular, we looked at the settings for VariantRecalibrator in this WDL. We ran germline analyses on samples...
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