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redo a variant calling run on a vcf
is this mode still works on** gatk4** of HaplotypeCaller and mutect2? if so, is there a recommended value of ip , thanks a lot
View ArticleHi, Is there any way to solve the data skew problem of HaplotypeCallerSpark?
Hi，Is there any way to solve the data skew problem of HaplotypeCallerSpark?
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Mutect2FilteringStats.tsv stands for what
when I ran gatk , there is a file Mutect2FilteringStats.tsv content likes following how should I understand this, thanks a lot
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urgent!!! HaplotypeCaller argument --bam-output bam does not keep a variant...
it is germline calling and this site is very important in chemotherapy， we need to have a accurate genotype of this site
View Articlehow to run CalculateGenotypePosteriors on a case-control cohort
One usage example is to refine genotypes based on the discovered allele frequency in an input VCF containing many samples gatk --java-options "-Xmx4g" CalculateGenotypePosteriors \ -V...
View Articlefastq reads cleaning
In the best practice for short variant discovery from DNA sequencing, there is no mention of reads cleaning (removing adapters, low quality and short reads, etc.) . I wonder whether it's because such...
View ArticleVQSR on SNP and Indel
My impression is that old recommendation from the GATK team is to do VQSR on snp.vcf and indel.vcf separately and in parallel. But the current pipeline and example is to do them sequentially on...
View ArticleHaplotype phasing somatic mutations from MuTect2 using read-backed phasing...
To whom it may concern, I have both normal and tumour sample and I also have the parental data (both mother and father) for the patient sample. I hope to first haplotype phase the SNP and INDELs from...
View Articlegvcf or final vcf used to construct accession specific genome
I have 100 rice accessions and its DNA sequencing bam files. My goal is to construct the genome in a specific region for each rice accession. Could I directly use the gvcf file from the variant call?...
View ArticleHow to pre-assign the multiple regions I want to process in each pipeline?
Dear Genome STRiP users, I intend to process part of the chromosome in each pipeline rather than processing the whole sequence. I know there is an -L flag in the SVPreprocess, but it is not listed in...
View ArticleIs the CNQ value the Phred quality score or the confidence percentile?
Dear Genome STRiP users, I completed the SVCNVDiscovery to all the samples in a single batch. Beside of the CN, I also got the CNQ for the CN of each sample. Based on...
View Articlehtsjdk.samtools.util.RuntimeIOException: {bqsr_bam_file} has invalid...
Hi! I'm using GATK4.0.7.0 and best practice workflow, where I first applied Base reacalibrator on my RNASeq bam-files. These seems to work fine (files are not truncated). Those bqsr-bam files now used...
View ArticleUnderstanding the math behind MUTECT LOD scores
Hello, thank you for making such great tools and having such a responsive forum for answering questions about your methods. My question is what are the LOD scores exactly and how are they computed (and...
View ArticleHow to Understand SVCNVDiscovery result: CN "-1" value with CNQ "." value
Dear Genome STRiP users, I got the CN and CNQ value by SVCNVDiscovery. After sorting the CNQ and the corresponding CN value, I found some weird CN values and CNQ values as below -- 10 samples out of...
View ArticleGATK
I'm running into an error when running GATK 4.1.0.0 with the following call: java -Xmx16g -jar ${gatkDir}/GATK.jar Mutect2 -R ${GRC}.fa -I ${TU}.recal.bam -tumor TU -I ${NM}.recal.bam -normal NM...
View ArticleHaplotypeCaller VCF entries with 0/0 genotype. How to interpret?
Hi there, I'm running HaplotypeCaller in version 4.0.10.0 using your cromwell pipeline which puts this command information in the VCF header: HaplotypeCaller --contamination-fraction-to-filter 0.0...
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What is a VCF and how should I interpret it?
This document describes "regular" VCF files produced for GERMLINE calls. For information on the special kind of VCF called gVCF, produced by HaplotypeCaller in -ERC GVCF mode, please see this companion...
View ArticleMutect2 files from TCGA - FORMAT tag [QSS] expected different number of...
Hi, I am trying to run vcf-validator (vcftools) on some VCF files I obtained from TCGA. These files are tumor-normal vcf files called using Mutect2. When I try and run vcf validator I get an error:...
View ArticleGATK4 does not include DepthOfCoverage tool
It appears that DepthOfCoverage is not listed as a tool for GATK4, I get the following error A USER ERROR has occurred: 'DepthOfCoverage' is not a valid command. I have searched through the list of...
View ArticleConcordance crashed
Dear Gatk team, I'm trying to compare two vcfs with genotypes for a single sample on two platforms using Concordance (gatk 4.0.1.1). Getting an error, please help: [jlr328@cbsurf01 Concordance]$...
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