Set Criteria for GVCF Blocks to Group by DP
Hi GATK, I know that currently GVCF Blocks group non-variant sites for which the genotype quality (GQ) is within a certain range. I was wondering if there is way to set the criteria for GVCF Blocks to...
View ArticleMESSAGE: Code exception (see stack trace for error itself) HaplotypeCaller
Hi, all: I meet some error while call variant with HaplotypeCaller, please help~~ Thanks a lot! my CMD: java -jar GenomeAnalysisTK-3.6.jar -T HaplotypeCaller -R...
View ArticleCollectHSmetrics
Hi everyone, Thank you in advance for reading this. Has anyone else had the following problem when running CollectHSmetrics: [Tue Apr 12 12:17:52 EDT 2016] picard.analysis.directed.CollectHsMetrics...
View ArticleGATK reports wrong allele
I downloaded the following BAM file: ftp://ftp.sra.ebi.ac.uk/vol1/ERA596/ERA596386/bam/Burkhardtshohle.bam I sorted and indexed the file with samtools. Then I created a VCF with the following command:...
View Articlecryptic invocationTargetException error
Hi, I am posting the full debug output here so that this hopefully can be solved quickly. I cannot figure out where the issue is here. I am running mutect-1.1.7, using this java version version...
View ArticleHow to choose the right threshold for VariantRecalibrator
Hi! I am using VQSR on a non-model species (88 whole genomes, following strictly the GATK best practices). For that I use a database containing ~40000 SNPs, obtained by genotyping by sequencing on 150...
View ArticleAnalyzing Bismark / Bowtie alignments with GATK (Hard vs Soft clipped data)
GATK team, is it ok to use GATK on BISMARK alignments? Given the caveats below? This is straight from the developers at babraham.ac.uk "In contrast to tools like GATK which specifically ask you not to...
View Articleg.vcf GQ of HOMREF block
I was looking at one of our g.vcf files, and I noticed the following homref block at the beginning of the file. END=195186 GT:DP:GQ:MIN_DP:PL 0:70:99:3:0,117 If I interpret this correctly, the block...
View Article--snpmask VCF format and nocalls
Hi everybody, I have been using FastaAlternateReferenceMaker to place variants back into a reference. To attempt to mitigate reference bias and restrict results to only confidently-called sites, I...
View ArticleGATK Indel Realignment and Base Quality Score Recalibration for Paired Samples
I have WES for tumor and normal paired samples. I did not do co-cleaning for the paired samples, I do not seem to have time to redo it, unless it would make much difference. Would it make much...
View Articlere-optimization.
HI!! I would like to ask regarding re-optimization scope of GATK framework. Is any related work is going on ?
View ArticleGALAXY installation.
There is error related initiation of job scheduler while executing GATK on GALAXY. Would you suggest any possibility of error?
View ArticleCould not find walker with name: SplitNCigarReads
Hello, When carrying out the SplitNCigarReads command I'm getting the following error message: ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name:...
View ArticleCram to Bam Conversion Lost MD:Z Tag (GATK 3.5)
I have been messing around with cram usage within GATK 3.5 and came across a dropped tag when converting from a cram file back to a bam file. Below is how I went about recreating the BAM file. java...
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Should I analyze my samples alone or together?
Together is (almost always) better than alone We recommend performing variant discovery in a way that enables joint analysis of multiple samples, as laid out in our Best Practices workflow. That...
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Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticlePicard Output Gives Malformed Bam and other files
I ran Picard with the following script without error, but when I ran GATK after that, I got error message that says the .bam file and .bai files are malformed. java -Xmx25G -Djava.io.tmpdir=tmp -jar...
View ArticleThe memory size I need to define while using -nt
For example, if I run java -Xmx10G -Djava.io.tmpdir=tmp -jar ${GATK} -T GenotypeGVCFs -nt 10 Does this mean I need to give the job 100G memory?
View ArticleFiltering for Homozygous Variants
Hello, I am trying to use an or statement to select for homozygous opposite genotypes between two samples in select variants. I have tried some variations but never been able to get what I am looking...
View ArticleIs the adapter boundary set correctly for overlapping read pairs?
Hi, I've been working on a GATK walker and during testing I noticed some discrepencies between the base counts from the ReadBackedPileup object I get from AlignmentContext.getBasePileup() and those I...
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