samtools vs picard for gatk analysis
Does it make a difference if the SAM file generated by BWA-MEM is sorted/converted to BAM using Samtools rather than PIcard to follwo up with GATK analysis?
View ArticleMost Variants Called
Hello all! So I am forced to do hard-filtering on my VCF files. Looking at them before filtering, ~99% of my variants have a QD of <2.0. Looking at the distribution plots in ggplot, they do not...
View Articlejava.lang.ExceptionInInitializerError in java.lang.ExceptionInInitializerError
Hello, We are trying to Run RealignerTargetCreator for 102 Bam files.Out of 102 bam files 14 files are showing the following error.I just want to know that the below issue is because of bam file or...
View Articlehow to run BaseRecalibrator Queue scripts in parallel
Hi there I am trying to optimise GATK BaseRecalibrator using Queue. I have read through GATK Forum, doc etc and implemented my Qscript (MyBaseRecalibrator.scala), which is as follows: package...
View Articlehaplotypecaller new version strand bias
Hi all, I am wondering how can we use the Strand bias annotation in new version? The argument -A StrandBiasSample is not available any more Please see the error message below. ERROR MESSAGE: Invalid...
View ArticleWhat's in the resource bundle and how can I get it?
NOTE: we recently made some changes to the bundle on the FTP server; see the Resource Bundle page for details. In a nutshell: minor directory structure changes, and Hg38 bundle now mirrors the cloud...
View ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
View ArticleGenotypeGVCFs Error:
Hi, I was trying to run GenotypeGVCFs with my data as follwing (version GATK 3.7): java -jar /var/bin/GenomeAnalysisTK.jar -T GenotypeGVCFs -R RefGenome.fa --variant a-45.g.vcf --variant a-8.g.vcf...
View ArticleCreateSequenceDictionary OutOfMemoryError
I'm running CreateSequenceDictionary on a Windows 10 machine with 4 gigabytes of ram and more than 50 gigabytes of free disk space, while my human dna reference file is nearly 3 gigabytes. The same...
View ArticleRedo / Recalculate gvcf bins
Hi GATK Team, I am wondering whether it is possible to redo the binning of a gvcf. For example if I have a gvcf created with the defaults the gvcf bins are 1 GQ 'wide'. Is it be possible to take this...
View ArticleAnalyzeCovariates error
Hi there, I'm trying to get AnalyzeCovariates to work, and I get the following error message...any thoughts as to what is going wrong? Not sure whether this is a program-related issue or not? Thanks!!...
View ArticleDepthOfCoverage takes many hours to run
I am using DepthOfCoverage on a targeted sequencing bam of 400 mbs, reading from hg19 (3 gbs), with an Intel core i3 2.0 ghz processor and 4 gbs of RAM. The remaining hours for completion are almost...
View ArticleGATK4: Trouble running "GATK 4 CNV Proportional Coverage for Capture"
Hi, I am trying to run "GATK 4 CNV Proportional Coverage for Capture" on samples with no matched normals sequenced using TSCA (TrueSeq Custom Capture). I understand that the first step is to run "GATK...
View ArticleSNP distribution across chromosome
Hi, I wonder to ask -is there any tool in the GATK to calculate SNPs/Indels distribution in each chromosome based on 100kb or 1 MB window size? Thanks.
View ArticleWhole Genome Sequencing and structural variation identification in human..
Hello, I have two queries regarding the structural variation identification using whole genome sequencing in human. If you can suggest, to identify structural variation (SV) like balanced chromosomal...
View ArticleRead groups
There is no formal definition of what is a read group, but in practice, this term refers to a set of reads that were generated from a single run of a sequencing instrument. In the simple case where a...
View ArticleWhole Genome Sequencing and structural variation identification in human..
Hello, I have two queries regarding the structural variation identification using whole genome sequencing in human. If you can suggest, to identify structural variation (SV) like balanced chromosomal...
View ArticleResults discrepancy (very low frequency mutation): GATK vs samtools mpileup...
I have a Plasmid library of random mutations (thousands of mutations), we performed targeted amplicon sequencing (high depth >7000) on Illumina's MiSeq platform. On performing variant calling with...
View ArticlePurpose and operation of Read-backed Phasing
This document describes the underlying concepts of physical phasing as applied in the ReadBackedPhasing tool. For a complete, detailed argument reference, refer to the tool documentation page. Note...
View ArticleHow can I invoke read filters and their arguments?
Most GATK tools apply several read filters by default. You can look up exactly what are the defaults for each tool in their respective Technical Documentation pages. But sometimes you want to specify...
View Article