MuTect2 with Queue
Hi, I'm trying to run Mutect2 with matched normal-tumor whole genome samples and I want to use Queue. I know it will take a lot of time with WGS samples and I want to use Queue as mentioned here...
View ArticleRemoving overlapping variants from one VCF file from another?
Hello! Firstly let me say the support in this forum is amazing and we are very lucky to have you guys listen and respond to our issues! I have illumina DNA sequening of bacterial populations which are...
View ArticleBWA ERROR on Terminal: [E::bwa_idx_load_from_disk] fail to locate the index...
Hi I have created the index files for my reference genome following the guidelines and had no errors. This is what I wrote: $PICARD CreateSequenceDictionary \...
View ArticleCombineGVCFs input multiple files
Hello, How can I specify the multiple input files for CombineGVCF without having to type the name of each file separately (I have 432 input files...)? Using java -jar GenomeAnalysisTK.jar \ -T...
View ArticleRelease notes for GATK version 3.7
GATK 3.7 was released on December 12, 2016. Itemized changes are listed below. For more details, see the user-friendly version highlights. HaplotypeCaller + GGVCFs 39da22b - Changes to use the median...
View ArticleStage 7 of CNVDiscoveryPipeline - all commands fail with...
I am attempting to run GenomeSTRiP's CNVDiscoveryPipeline. I have run SVPreprocess successfully and am now running CNVDiscoveryPipeline on a single chromosome. Each command at stage 7 fails with the...
View ArticleVersion highlights for GATK version 3.7
Here it is at last… as in, last release for 2016, and possibly the last point release of GATK 3 ever! Aside from the usual pile of bug fixes, the new features in this version are actually (almost) all...
View ArticleRNAseq varaint calling error
I'm following the Calling variants in RNAseq algorithm and I'm having an error message during the Split'N'Trim and reassign mapping qualities step. The command I'm using is: java -jar...
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MuTect2 misses a deletion that is obvious in IGV
Hi, first of all, thanks for GATK! I am using MuTect2 and it works well overall. In one of our samples, however, we know that a deletion exists at 1:23559238. It is also clearly visible in IGV for the...
View Article1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf corrupted?
Hi i downloaded the file from GATK google cloud but it seems the file is corrupted? only chr1-chr15 sites are present.
View Articlecosmic.vcf.idx is not right for MuTect1
I want to call somatic mutation by mutect1, but I can't find cosmic.vcf in ftp ,and I want to use new version.So step1:download new version file cosmic get...
View Articleerror message
hi i am getting following error message on linux system Please Check Error: iontorrent@iontorrent-PowerEdge-T420:~/NGS_run_sagar/bwa$ java -Xmx8G -jar...
View Article(howto) Install and run Oncotator for the first time
1. Download the Oncotator package, the default datasources package, and (recommended) transcript override list from the Downloads page Please note: Broadies who wish to run the installed Oncotator on...
View ArticleDescription and examples of the steps in the CNV case and CNV PoN creation...
The CNV case and PoN workflows (description and examples) Requirements Java 1.8 A functioning GATK4-protected jar (hellbender-protected.jar or gatk-protected.jar) HDF5 1.8.13 The location of the...
View ArticleGATK3.7 GenotypeGVCFs Runtime Error
Hello. I am attempting to perform joint genotyping on .g.vcfs from approximately ~9000 exomes (combined with CombineGVCF into ~200 sample chunks). My estimated runtimes when using GATK3.6 were on the...
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MuTect2 output - number of Variants expected to PASS the test
Hi, I have just done a Variant Calling using MuTect2 with 10 samples coming from GDC data portal and their respective matched-normal, with a PoN of 12 samples. I'm just a little confused about the...
View ArticleBest approach for realignertargetcreator and indelrealigner
Hi, I am trying to decide between two approaches for performing realignment around indels. I have ~600 samples that have been aligned to a very fragmented draft genome assembly. What is best: 1. take...
View ArticleHRAS gene is not unique in hg38?
I would like to mention an unusual problem I run into when doing variant calls on thyroid cancer sample with HRAS Q61R mutation (see attached IGV screenshot. Mutect2 did not call this obvious variant....
View ArticleHow do you download GATK using ansible script?
I've been fighting this for a little while and I think this is something you should consider strongly if you haven't already. How can one download GATK set of tools non interactively e.g with wget...
View ArticleMutect2 Somatic mutation genotype is not like HaplotypeCaller genotype
I use mutect2 (version 3.7) to detect somatic mutation, got the result, but I find the GT is not like HaplotypeCaller。 such as 0/1:0,77 ,genotype is 0/1, and ref depth is 0 , alt depth is 77 , in...
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