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(howto) Generate a "bamout file" showing how HaplotypeCaller has remapped...
1. Overview As you may know, HaplotypeCaller performs a local reassembly and realignment of the reads in the region surrounding potential variant sites (see the HaplotypeCaller method docs for more...
View ArticleError handling end exit codes in GATK
I have a question regarding the error handling of GATK. Is GATK always returning a 0 exit status? For example one of my bam files seems to be malformated, so the Haplotypecaller reports an error and...
View ArticleWhy does GATK LeftAlignAndTrimVariants set a missing genotype to 0/0?
Hi. I appreciate many your helps. I have one vcf file (a.vcf). This file has one variant data. The data also has missing genotypes "./." because of DP=0. The variant is tri-allelic variant as below....
View ArticleOncotator Most Recent Version and Data Source
Where can I download the most recent version of Oncotator, and data source? v1.9.1.0?
View Articleerror concerning vcf file with dbSNP in base recalibration
I am running BaseRecalibrator in GATK 3.6 for mouse mm10, using dbSNP 142 for mm10, and am getting this error: "The provided VCF file is malformed at approximately line number 11959: VCF support for...
View ArticleHow do I apply depth filtering..?
I would like to apply hard filtering based on read depth at Ref allele or Alt allele supporting level. Could someone guide me to achieve the same. For example, 10 read should support variant allele,...
View ArticleUnifiedGenotyper error: Somehow the requested coordinate is not covered by...
Dear GATK Team, I am receiving the following error while running GATK 1.6. Unfortunately, for project consistency I cannot update to a more recent version of GATK and would at least wish to understand...
View ArticleJoint calling cases/controls
Dear Team, I have aprox.100cases and 100controls (WES). Would you rather run joint calling (according to GATK best practises) on cases and controls separately or jointly call cases and controls? If I...
View ArticleWhat's in the resource bundle and how can I get it?
NOTE: we are currently working on overhauling the bundle to 1) add support for Hg38 and 2) document the provenance of the resource files more fully. 1. Accessing the bundle See the Resource Bundle...
View Articlepicard.sam.MergeBamAlignment fails
Hello, I'm a new user to Picard. I am running Picard as part of a pipeline in Drop-Seq. My command is [Thu Nov 24 08:22:35 EST 2016] picard.sam.MergeBamAlignment...
View ArticleIndel Realignment still needed for GenomeSTRiP?
Indel Realignment is no longer a recommended best practice step for the GATK pipeline to call genotypes with HaplotypeCaller. However, doesn't indel realignment still need to be run to prepare bams for...
View ArticleDownsampling
Downsampling is a process by which read depth is reduced, either at a particular position or within a region. Normal sequencing and alignment protocols can often yield pileups with vast numbers of...
View ArticleError parsing text SAM file. Empty sequence dictionary.; File...
I am trying to remove rRNA sequences from my fastq files. I built the rRNA index file with bowtie-build, then mapped my reads to the index file producing .sam files. Then used: samtools view -f 4...
View Articleerror_java.lang.IllegalArgumentException: No data found--when using VQSR
ERROR ------------------------------------------------------------------------------------------ ERROR stack trace java.lang.IllegalArgumentException: No data found. at...
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...
View ArticleGenotypeGVCFs java error; java.lang.NegativeArraySizeException
Hello! I used the following command to run GATK GenotypeGVCFs. (GATK version : nightly-2016-11-23-g69e703d / Java : Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14)...
View ArticleMuTect2 sample names
My MuTect2 VCF records header looks like this: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL The samples are named TUMOR and NORMAL rather than by the actual names. It doesn't appear like...
View ArticleSelectVariants Error
Hello, While trying to use SelectVariants to filter for AlleleFrequency, and trying multiple different ways of writing the expression with and without spaces etc and following the SelectVariants...
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(How to) Generate an unmapped BAM from FASTQ or aligned BAM
Here we outline how to generate an unmapped BAM (uBAM) from either a FASTQ or aligned BAM file. We use Picard's FastqToSam to convert a FASTQ (Option A) or Picard's RevertSam to convert an aligned BAM...
View ArticleHow to get output in java script
Hi, I'm trying get output of gatk function. I thounk during 3 days that a common solution resolve my probleme as : ByteArrayOutput baos = new ByteArrayOutputStream () Printstream ps = new Printstream...
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