Dog breed genetics/health committee: Recently received 8 canine genomes (4...
I’m a microbiologist with limited computational/bioinformatic training ( but can hack it when necessary with prokaryotic genomes). However, I recently was given a committee position within an AKC dog...
View ArticleSpeed up HaplotypeCaller on IBM POWER8 systems
We all know how HaplotypeCaller and Mutect2 analyses can take a long time. IBM is now providing a native implementation of the PairHMM algorithm that leverages the new hardware available in their...
View ArticleUnclear ERROR message
Dear GATK Team, I have performed a parallel analysis of > 200 samples with Haplotype Caller in gvcf mode on a computing cluster. All but two files yielded no error. For these two, I got the...
View ArticleClik here to view.
Spanning or overlapping deletions
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 ArticleMay I get the old format for reporting a spanning del using GATK 3.6?
At the bottom of page http://gatkforums.broadinstitute.org/gatk/discussion/6926/spanning-or-overlapping-deletions? two different ways to report spanning deletions in vcf files are shown. Is there a way...
View ArticleMuTect2 tumorOnly vs paired loses true variants
Hi GATK team ! I have an issue with MuTect2. I'm using GATK last version (nighlty build from 16th of March) in a somatic context on an amplicon design. I have a variant that I know is true one...
View ArticleMutect variant calling the parameters for filtering
Hello All, I have a couple of vcf files resulted from a batch run from the pipeline from the Mutect and I wanted to filter the output cf file based on the following parameters...
View Articlevariants predicted by HaplotypeCaller with DP=0
Hello, We found two variants predicted by HaplotypeCaller with DP=0. We also generated --bamout for the variant regions. However, we didn't found output for these regions (attached, the first track is...
View ArticleGATK Depth of Coverage randomly crashes?
Hi everyone, Thank you for reading! I'm running GATK (v3.6-0-g89b7209) DepthofCoverage on a list of bam files. I originally had my files separated as a list of 23 paired bams for normal and tumor but I...
View ArticleThe error of Mark Dupplicate
I run the step of Mark Duplicate in the server, but it always print an error message even though I changed server. This is my input: java -jar /home/yangguoqian/biosoft/picard-tools-2.5.0/picard.jar...
View Articlevariation info found in bam but not in final vcf file
Why veiw the bam by samtools, there is snp variation on one position,but in the final vcf file, there is no variation result on that position. please kindly see the following sample NA12878-580ng-2 for...
View ArticleGenotypeGVCF Parallelism
Hello, I am trying to do joint genotyping with GenotypeGVCF on about 250 exomes. I tried to look at the docs to see the best way to paralyze this process, but didn't find a clear answer. Are nt and nct...
View ArticleRNA-SeQC/GATK: IntronicExpressionReadBlock error
Hello, I seem to have the same error as the one posted 14 days ago on BioStar (https://www.biostars.org/p/208982/). Had successfully run this command in June: java -jar RNA-SeQC_v1.1.8.jar -o rnaSeQC...
View ArticlePicard tools MarkDuplicates using cram format ...How to pass A valid CRAM...
Hello there! I am trying to use picard tools to mark duplicates using a cram format file; however I could not find any documentation to address this problem. How can I pass a valid CRAM reference?...
View ArticleFinal VCF is skipping sites covered by the intervals and the ALT allele...
Hi GATK, For GATK version 3.6, I have come across two issues. First, I have noticed that there are many positions that do not show up in my final VCF, even though they are covered by the interval file...
View ArticleHashMap iterator problem with GATK 3.6 on NA12878 validations
Hi all; I was running validations with the latest GATK 3.6-0 release and ran into an issue on NA12878 where a region around the centromere on X fails with a HashMap NoSuchElementException. I tried to...
View ArticleMarkduplicates in Cram files. A valid CRAM reference was not supplied...
Hello, I wonder if you can help with the following. I am trying to mark duplicates in a cram file with the following command (picard latest): 'picard-tools MarkDuplicates I=09_1#21.cram...
View Article(howto) Map and mark duplicates
See Tutorial#6747 for a comparison of MarkDuplicates and MarkDuplicatesWithMateCigar, downloadable example data to follow along, and additional commentary. Objective Map the read data to the reference...
View Articlecannot use SelectVariants to combine VCF files
I try to use SelectVariants to find concordance between two VCF files, one generated from GATK UnifiedGenotyper and the other from samtools mplieup. But I get error message showing the samtools VCF...
View Articlemore 512M chromosome problem in GATK
i use GATK to deal with Wheat_survey genome which have a 3B chromosome(700+M), it can`t call snp from 512M to 700M use default paramaters, how fix it???
View Article