MuTect2 and VQSR: anyway of calling VQSLOD for MuTect2 ?
Hello GATK Team ! @Sheila @Geraldine_VdAuwera Since my last question ( here ), I am trying to build a workflow which can process all my samples with a snakemake workflow. From the previous question...
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热烈欢迎我们的中国朋友 / A warm welcome to our Chinese friends
科研圈的亲们，我们来啦！携手国内重量级公司和机构，我们这次给大家带来了高效、规模化使用GATK的技巧！ Today we are reaching out to the Chinese research community with great news: we are partnering with key companies and institutions in China to...
View ArticleMutect2 error: Code exception (see stack trace for error itself)
Hi, I'm trying to run Mutect2 (GATK v3.7-0-gcfedb67 - installed via conda) on a tumour normal pair with a panel of normals. As a first step (following this) I'm calling each normal sample individually,...
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Errors in SAM/BAM files can be diagnosed with ValidateSamFile
The problem You're trying to run a GATK or Picard tool that operates on a SAM or BAM file, and getting some cryptic error that doesn't clearly tell you what's wrong. Bits of the stack trace (the pile...
View ArticleBatch v joint calling for smaller cohorts?
Within Illumina's Basespace you can only do variant calling on up to 96 samples at any one time using the app BWA Enrichment - so you'd have to do batch calling for a larger cohort. Is joint calling a...
View ArticleBwaAndMarkDuplicatesPipelineSpark Input Format
Hi, looking forward to GATK_4 release, so I have started investigating 4 beta1. I like the tools that are available, calling method and Spark! I had therefore set up a Spark pipe of...
View ArticleError details: SAM file doesn't have any read groups defined in the header....
Hello I am new to GATK and I am attempting to follow the best practices for germline SNPs and Indels in Whole Exome sequencing. Here is my code: import os, pprint path =...
View ArticleTutorial files provenance: ASHG15
This document is intended to be a record of how the tutorial files were prepared for the AHSG 2015 hands-on workshop. Reference genome This produces a 64 Mb file (uncompressed) which is small enough...
View ArticleUnifiedGenotyper miss some alleles while using GENOTYPE_GIVEN_ALLELES mode
Dear GATK team, We are using UnifiedGenotyper GENOTYPE_GIVEN_ALLELES modes to do genotyping, but we found that not all given alleles were genotyped. For example, the input vcf is: 13 20763485 . AG A 30...
View Articlejava.lang.ArrayIndexOutOfBoundsException: 83 running MuTect
Hello. I am getting a java.lang.ArrayIndexOutOfBoundsException: 83 error when running MuTect. I got this error on v1.1.4 and built the latest version this morning (v1.1.7) but the error is still there....
View ArticleArrayIndexOutOfBoundsException Mutect2
[Sorry for the repost - I can't seem to be able to edit my original question - asked yesterday] I'm trying to run Mutect2 (GATK v3.7-0-gcfedb67 - installed via conda) on a tumour normal pair with a...
View ArticleAre low frequency SNPs reported using the halpotypeCaller?
Dear all, If I understood correctly, the halpotypeCaller is not for calling low frequency SNPs - that would be Mutect, correct? However, how low is too low for the halpotypeCaller? Is there a certain...
View ArticleGenotypeGVCFs: no records in VCF
Dear GATK team, I am having troubles calling genotypes on *.gvcf produced by HaplotypeCaller in GVCF mode. When I run GenotypeGVCFs (GATK 3.5), I get only header in resulting VCF file, but no records....
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Impact of VQRS variant set size on model
Hi, We are evaluating the option to gather a set of 'good reference samples' to function as additional data in the VQRS step during WES analysis. We would like to do so, since we receive trio-based...
View ArticleHaplotypeCaller and GenotypeGVCFs sensibility on heterozygous variants
Hello, I recently compared results from GATK best practices (bwa, Picard, HaplotypeCaller, GenotypeGVCFs) with a snp array set (a high confident known variant detection method) for 6 samples (data from...
View ArticleFisher or SOR?
Hi, the SOR-documentation says: It is an updated form of the Fisher Strand Test that is better at taking into account large amounts of data in high coverage situations. so to clarify: the SOR is better...
View ArticleQuestion about retries when using Google Cloud Storage
I am wondering what GATK's method is for retries upon GCS failures and whether GATK is the one that will retry, or if this is something the user of the tool should do. Here is an example of failure to...
View ArticleBest Practice presentations?
Hi, I'm trying to find powerpoint presentations from previous best practice seminars. Links on the website which seem like they should go to a pdf, instead go to a page with a calendar of seminars. For...
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Firecloud can't decide if a workflow is running or not..
I get one view in the "monitor" tab : and another when I chose a particular "running" workflow: Is this a bug? can I do something about it?
View ArticleProblems running ExtractIlluminaBarcodes and/or IlluminaBasecallsToSam
I've been trying to use picard tools to demultiplex directly from Illumina base calls to unmapped bam files, with no success. I have a slightly unusual setup with dual (sample) barcodes on the reads,...
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