How could I get the SNPs commonly identified by both GATK and SAMtools ?
Hi, I use GATK and SAMtools to perform SNP calling, then I got two .vcf files: GATK.vcf & SAMtools.vcf. One is from GATK and another is from SAMtools. I want to get the SNP commonly identified by...
View Articleduplicates are not filtered out by picard 2.2.1 MarkDuplicates
I analyze sequences from FFPE, so some of them are low quality or short sequences (< 100nt). my pipeline includes the following steps: bwa mem -t; samtools view -b; samtools sort; picard.jar...
View ArticleAnnotating StrandOddsRatio for files created outside GATK
Hi, I'm trying to compare variants identified in GATK and samtools with respect to variant attributes. I'm wondering how to add StrandOddsRatio annotations to a samtools generated VCF file. When I use...
View Article(Howto) Run GATK4 in a Docker container
1. Install Docker Follow the relevant link below depending on your computer system; on Mac and Windows, select the "Stable channel" download. Run through the installation instructions and initial setup...
View ArticleMinor Allele Frequency filter in GATK
Hi all, I'm working on a resequencing dataset , which contains 60 individuals from 5 different populations. I used HaplotypeCaller to conduct variants calling, and got all individuals in one big...
View ArticleGermline CNV Tutorial available?
Is there a tutorial available for calling CNVs in germline DNA with GATK4? I see an earlier post for somatic CNVs but could not locate one for germline CNVs.
View ArticleHow do I specify a list of samples for GenotypeGVCFs?
This is the recommended code for GenotypeGVCFs java -jar GenomeAnalysisTK.jar \ -T GenotypeGVCFs \ -R reference.fasta \ --variant sample1.g.vcf \ --variant sample2.g.vcf \ -o output.vcf Is there some...
View ArticleUse all samples or group samples for GenotypeGVCFs?
I have created g.vcfs for all my samples (48). Half of my samples (24) are control individuals and the other half (24) is treated individuals. Should I run GenotypeGVCFs on all my samples once to...
View ArticleInsert length filtering problem
Hello, I'm following the HaplotypeCaller pipeline for SNP and indel calling, however, I'm facing the following problem. The sequence I'm analyzing has two copies of the same gene with reverse...
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Understanding the HP tag in read backed phasing
Hi there, I have used haplotypecaller best practices to obtaine the vcf file. Next I used read backed phasing to phase my vcf file, however I am not able to properly understanding the results, e.g....
View Articleexit code -9
I am doing bqsr and got an "exit code -9" error, what does this code mean? Thanks
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GenotypeGVCFs with same RG tags
Dear GATK forum, Could you please clarify GenotypeGVCFs behaviour when some gvcfs share the same RG tag? in scenario 1 (vertical): we have split single sample into 5 chromosomes using HaplotypeCaller...
View ArticleGATK4 importGenomicsDB multiple lanes per sample
I've been trying to genotype a set of samples using GATK4. Some samples were sequenced in multiple lanes, so they have multiple fastq files. I've been keeping each individual lane separate, but keeping...
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Genotype Refinement workflow
Overview This document describes the purpose and general principles of the Genotype Refinement workflow. For the mathematical details of the methods involved, please see the Genotype Refinement math...
View ArticleConversion of vcf to gvcf
I am trying to combine and convert two VCF 4.1 files (an SNP VCF and an INDEL VCF) to VCF 4.2 (which, if I understood correctly is the same thing as gVCF). The resulting file would then be used as...
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View ArticleMutSig categ discovery failure
HI I am using the mutsig to analyze my data. I not that mutsig has an preprocess step to calculate the categ column from the MAF input file. This step requires a genome reference file for its...
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Problem using GATK4 GenomicsDBImport for joint calling.
Hi, I am trying to use GATK4 for joint-calling. I am calling variants by HaplotypeCaller in GVCF mode for three samples (HG002-3-4). I am using HaplotypeCaller parallelized using scatter-gather method...
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"> I don't know if there will be much of a difference in the amount of phased sites, but you should really run per-chromosome or per-genome because of the reasons Geraldine mentioned in the thread...
View ArticleERROR MESSAGE: java.lang.reflect.InvocationTargetException
Dear GATK team member, When I used the GenomeAnalysisTK.jar, the "ERROR MESSAGE: java.lang.reflect.InvocationTargetException" appeared. Could you please tell me how to fix it? Thanks a lot! the code is...
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