someone help me
[Mon Nov 14 14:47:57 SAST 2016] picard.sam.SortSam done. Elapsed time: 75.95 minutes. Runtime.totalMemory()=3131047936 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp...
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The GATK Best Practices for variant calling on RNAseq, in full detail
We’re excited to introduce our Best Practices recommendations for calling variants on RNAseq data. These recommendations are based on our classic DNA-focused Best Practices, with some key differences...
View ArticleHow to interpret output of ContEst
Hi! I've recently started using ContEst and now I'd like to understand exactly what I get in the output file. What does each column mean? Specifically: -Are "contamination",...
View ArticleIs it too early to be publishing data analysed by MuTect2?
Is it too early to be publishing data analysed by MuTect2 in a comparative sense with Haplotype Caller? Is it still strictly in testing phase?
View Article(howto) Prepare a reference for use with BWA and GATK
NOTE: This tutorial has been replaced by a more recent version that uses GRCh38 that you can find here. Objective Prepare a reference sequence so that it is suitable for use with BWA and GATK....
View ArticleCollected FAQs about input files for sequence read data (BAM/CRAM)
1. What file formats do you support for sequence data input? The GATK supports the BAM format for reads, quality scores, alignments, and metadata (e.g. the lane of sequencing, center of origin, sample...
View ArticleHow can I exclude snp sites with ALT asterisk by SelectVariants ?
Hello , I am using the latest GATK 3.6 to analysis my human WGS data. For snp analysis, when I ran VariantRecalibrator , it reported error as following: 1 788419 . A * 854.77 PASS DP=33 GT 0/1...
View Articlereference sites FORMAT output
Is it possible to report GT:AD:DP:GQ:PL for sites with reference calls just like the sites with snp/indel calls? In the example below, I have a position with reference call and a position wiht indel....
View ArticleDoes PrintReads accepts gz bam files ?
I am feeding a list of BAM.gz files into PrintReads to get a subset of BAM files for a region. I get this error message ! ERROR MESSAGE: SAM/BAM/CRAM file BL01.sorted.dedup.rlgn.bam.gz is malformed....
View Articletumor normal pair
Dear GATK team, I am a little bit confused about the Tumor Normal pair branch of GATK using haplotypecaller. We are recommended to re-align tumor sample and its normal control at the same time. As a...
View ArticleHaplotypeCaller does not call variant depending on the interval list I use.
I am trying to explain why HaplotypeCaller calls a variant in some cases but not in others. I notice that a FN had very good coverage (>2000x) but wasn't being called. I ran HaplotypeCaller using an...
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'a malformed header' error message with known indel vcf
Hi! One of the Indel reference vcf files, which I'm trying to use for '-known' argument during RealignerTargetCreator step, gives me an error and I'm not sure how to solve this problem. (I've searched...
View ArticleSelectVariant JEXL expression to select private variants from multisample VCF
Dear all, I hava multi-sample VCF file from which i need to extract shared private variants(variants shared only a specific group) . I have used the below command to find shared variants. java -Xmx4g...
View ArticleDifference between no variant and no data.
Hello all! After creating VCF files for each of my samples individually, I compared variants and found that some samples have called tens of thousands more than their genetically identical siblings...
View ArticleArray index out of bounds exception in RealignerTargetCreator
INFO 01:05:48,346 HelpFormatter - -------------------------------------------------------------------------------- INFO 01:05:48,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-ge91472d,...
View ArticleGATK calling on del/ins at same location
Hi there, I mapped using both BWA and novoalign. In my sample on gene DHCR7 on chr11, there is Deletion and Insertion at same location. Del of 4 bases (GACG) at chr11: 71,155,132 - 71,155,135 AND...
View Article(howto) Recalibrate variant quality scores = run VQSR
Objective Recalibrate variant quality scores and produce a callset filtered for the desired levels of sensitivity and specificity. Prerequisites TBD Caveats This document provides a typical usage...
View ArticlePipelining the GATK with Queue
1. Introduction As mentioned in the introductory materials, the core concept behind the GATK tools is the walker. The Queue scripting framework contains several mechanisms which make it easy to chain...
View ArticleIs Mutect2 in GATKv3.6 still a beta version?
Is Mutect2 in GATKv3.6 still a beta version?
View ArticleSVPreprocess error
Hi Bob and all, I try to use the GenomeSTRiP recently. I got some error while I am running SVPreprocess. I modify the installtest/discovery.sh as my svpreprocess script. Here are the script content :...
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