Does 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 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 Articledefine java to use in GATK4?
Hi, today I tried to run GATK4. But I ran into an issue. Just calling "gatk" looks fine, but when running "gatk --list" produces the following output. Running: java...
View ArticleInvalid or corrupt jarfile
Hi， My system is Linux, and java is "java version "1.8.0_45". I download the gatk-4.0.1.2.zip and unzip it, then I run ./gatk --list，the error occurs： Using GATK jar...
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[Picard] Read error; BinaryCodec in readmode
Dear, GATK team. Could I ask something related to picard program in here? java -Dsamjdk.compression_level=5 -Xms16000m -jar /BiO/BioTools/picard-2.17.8/picard.jar \ SortSam \...
View ArticleGenomicsDBImport too slow on local server
Hi, I tried using GenomicsDBImport for our data. In my testcase I tried importing Chromosome 1 for 223 samples. Since most samples are panels and we have only a few genomes and exomes, I thought it...
View ArticleQD Annotation error in GATK in VariantRecalibration step
hi all, i downloaded a BAM file from 1000 genomes to work on and converted it to FASTQ and aligned with bwa mem to hg38, this worked fine. later I wanted to run VariantRecalibration and use the...
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Strange behaviour (bias?) in BaseRecalibrator
Hello, I would like to report a possible weird behaviour of GATK BaseRecalibrator. During my analyses I follow the suggested "Best Practices", so after aligning I mark the duplicates (if needed) and...
View Article[GATK 4.0.0.0] Allelic copy number
First, thank you very much for this great tool (GATK4). Copy number profil even with targeted sequecing are now much more accurate with or without a matched normal. But now i wonder if it's possible to...
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(How to) Call somatic copy number variants using GATK4 CNV
This demonstrative tutorial provides instructions and example data to detect somatic copy number variation (CNV) using a panel of normals (PoN). The workflow is optimized for Illumina short-read whole...
View ArticlePicard: FixMateInformation crash
Hello, I was asked to re-post this question here. It was originally posted in the Picard forum at GitHub at https://github.com/broadinstitute/picard/issues/161. Regards, Bernt ORIGINAL POST (edited)...
View ArticleWGS+WES combined discovery/genotyping
Hi GATK team, Hope you had great holidays! We're analyzing small families where some individual have been sequenced by WES (HiSeqX) and others by WES (HiSeq4000). Could you please advise on the best...
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Missing or Inconsistent call between single-sample and multi-sample SNP calling
Dear all, I have generated a gVCF file using HaplotypeCaller (v3.7)and searched for a specific variant of interest which looks like below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT N417 chr1 627033...
View Article[Publish] Publish my own WDL including GATK
Hi, I have several tested WDL scripts including some GATK command lines and PUBLIC GATK docker images. Could you please let me know whether I am allowed to pulish them on FC so that more people can...
View ArticleGATK4 resource bundle
Hi, I was wondering if you guys are planning to release a new resource bundle with full hg38 support (+patches)? Perhaps to celebrate the release of GATK4? Thanks M
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(How to) Map reads to a reference with alternate contigs like GRCh38
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section. This exploratory tutorial...
View ArticleValues for QD annotation not detected for ANY training variant in the input...
Hi, I am running VariantRecalibrator on 2 WGS using the command: gatk VariantRecalibrator \ -R ./hg38/Homo_sapiens_assembly38.fasta \ -V combinedgVCF.g.vcf.gz \ --resource...
View ArticlePICARD MarkDuplicates errors near the end of its process: tmp does not exist
Hi, I have a problem in that PICARD MarkDuplicates appears to error near the end of its process -- with a temp file not found error. This is running in a GATK pipeline on our cluster for WGS Best...
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Spanning or overlapping deletions (* allele)
We use the term spanning deletion or overlapping deletion to refer to a deletion that spans a position of interest. The presence of a spanning deletion affects how we can represent genotypes at any...
View ArticleDifferences between CollectFragmentCounts and CalculateTargetCoverage
Good afternoon, I was hoping somebody could help illuminate the differences/similarities between CollectFragmentCounts (4.0 official release) and CalculateTargetCoverage (4.3 Beta). Are these the same...
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