RealignerTargetCreator 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 Articlecan depth of bam file at some position is lower than depth of vcf?
I aligned reads to reference with BWA-mem and called variants using HC. In my understanding, depth of bam can be reduced in vcf file because of some filtering options. However, can depth of bam file at...
View ArticleHaplotype caller (GATK 3.7) warning message for InbreedingCoeff
Hi, I am running HC with both .g.vcf and bamout as parameters. The command executes successfully, but with warning message: Annotation will not be calculated. InbreedingCoeff requires at least 10...
View ArticleError when running CNVDiscoveryPipeline using the latest version(SVToolkit...
Dear @bhandsaker I have finished running the deletion discovery pipeline, but when running CNVDiscoveryPipeline using following command, it gave me an error. It is difficult for me to figure it out....
View Articlecan i determine total count for a snp using HaplotypeCaller Tool?
Hello I am interested in finding the total number of reads supporting each snp found by the HaploTypeCaller tool. I just find the DepthOfCoverage tool which has the --countType COUNT_READS option. It...
View ArticleNot sure if bug or user error
I am using the GATK best practices for germline SNPs and Indels in Whole Genomes and Exomes and I get the following error when I try to use this command: os.system('java -Xmx6g...
View ArticleAF calculation in Mutect2
Hi, I've been calling somatic mutations with Mutect2, and have noted that the AF calculation does not always correlate to DP alt/(DP ref+DP alt). For example, consider this indel: T057.mutect2.vcf:7...
View Articlehuge time difference between HC and UG against 2000 known variants
Hi, We are doing the benchmark analysis against amplicon sequencing data for 2000 known variants. Both HC and UG have been tried. However, it seems that HC take much longer time than UG, which is not...
View ArticleClean version of dbSNP in the GATK resource bundle
Hi I understand that version 129 of dbSNP is considered clean and does not share data from other databases such as 1000G projects. What steps of the variant calling in WGS/WES analysis can be affected...
View Articlebest practices for calling snps from RNAseq reads mapped to denovo transcriptome
Dear GATK community, I would like to use GATK to call SNPs from RNAseq reads (from 7 libraries) mapped to a de novo transcriptome assembly (no reference genome available). I am having trouble finding...
View Articlerunning gatk snp call in KNL computing node (Intel Xeon Phi 7250)
Hi there, I would like to run gatk SNP call in TACC stampede2 machine (https://portal.tacc.utexas.edu/user-guides/stampede2) and they have the KNL node equipped with Intel Xeon Phi 7250. This CPU is...
View ArticleUnknown Contig problem with SplitNCigarReads
Hi everyone. I'm trying to run SplitNCigarReads on my STAR-aligned samples (using galaxy servers) that have gone through steps of Marking Duplicates & Sorting via Picard. Whenever I try to run...
View ArticleArrayIndexOutOfBoundsException in GenotypeGVCFs on chrX with male/female...
I am attempting to call exomes using GATK 3.8, the new quality model, and AS annotations. However, for chrX, I get an ArrayIndexOutOfBoundsException for chrX, likely as I am using different ploidy for...
View Articlepicard 2.10.7 fails pipelining SortSam and SetNmAndUqTags
Hi. I just upgraded to picard 2.10.7 and doing my regular exome work however I noticed this problem under 2 different platforms. 18:12:17.734 INFO NativeLibraryLoader - Loading libgkl_compression.dylib...
View ArticleShould CheckIlluminaDirectory be able to handle a non-standard read structure
I have a flowcell (from a 10x library) in which the 'natural' read structure is 178T8B14B5T. However, I want to interpret the flowcell as 178T8B14T5S, so that is what I passed to...
View ArticleHow to use bwa mem for paired-end Illumina reads
Dear All, we would like to use the bwa mem algorithm for the alignment of paired-end (100 bp) Illumina reads and variant calling with GATK. Unfortunately there are some problems understanding the...
View ArticleIntervals and interval lists
Many of our workflow recommendations and example commands involve intervals or lists of intervals, which you can specify in your command line using -L (or -XL to exclude specific intervals). So where...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleContest error: mismatched contigs
Hello, I've downloaded bams from dbGaP, that were aligned to grch37. GATK Contest tool is saying mismatched contigs when using hg19. Is there a different reference I should use, if yes, which one? If I...
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