Variant filtration by allelic balance bias
Hi everyone, I'm trying to find a way to filter some heterozygous genotypes that might have been misassigned due to PCR or sequencing errors and result in a very unrealistic allelic balance bias like...
View ArticleuBAM - Unmapped BAM Format
uBAM is a variant form of the BAM file format in which the read data does not contain mapping information. This is basically an "off-label" use of the BAM format (which was specifically designed to...
View ArticleCan't analyze simultaneously
Hi, I have trouble about analyzing of BAM file with Picard FixMateInformation(Version: 2.20.1-SNAPSHOT) I tried to analyze 30 samples simultaneously with supercomputer , but some samples are not...
View ArticleCompressed output file size from GatherVcfs is different when input files are...
I have produced gVCF files for different intervals from the same sample (using the -L flag) and now want to merge those smaller VCFs together, to create one single large gVCF per sample, using...
View ArticleCNVDiscovery Stage 7 errors
Dear all We have run into a problem while running CNVDiscovery. The errors are occurring during Stage 7. An example of the type of error can be seen below: ERROR 00:13:56,742 FunctionEdge - Error:...
View ArticleCan the new Mutect2 (version >4.1.0.0) support a GVCF output?
Hi, I was wondering if the latest version of Mutect2 can now support a GVCF output. According to a blog titled "Short Variant Caller Roundup" from last February: "The GATK 4.1.0.0 release introduces a...
View ArticleHelp with FastaAlternateReferenceMaker for converting VCF to fasta
I am having some trouble running the FastaAlternateReferenceMaker tool to convert my vcf sequences to fasta using a reference genome. I started with a multi-sequence vcf made from whole genome...
View ArticlePicard ValidateSam exit status 3
Hello. I am trying to get a better understanding of the exit status codes for ValidateSam. I was running the command within a snakemake pipeline, and clearly there are some errors with the bams...
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(How to) Run the Pathseq pipeline
Beta tutorial Please report any issues in the comments section. Overview PathSeq is a GATK pipeline for detecting microbial organisms in short-read deep sequencing samples taken from a host organism...
View ArticleVQSR: Bad input: Values for DP annotation not detected for ANY training...
Hi team, I'm have a vcf callset file generated using HaplotypeCaller in --emitRefConfidence GVCF mode with subsequent GenotypeGVCFs. I used the generated output.vcf file as input for...
View ArticleLiftoverVCF chain file for b37 to hg38
For liftover of a b37 vcf to hg38, the gatk LiftoverVcf tool needs a chain file (b37Tohg38.chain). The documentation example uses this file but I don't see it in the GATK bundles. Is there one...
View ArticleConfusion over newer Mutect2 tutorial,
Dear Mutect team, At the start of this link it says that this tutorial had been deprecatedhttps://software.broadinstitute.org/gatk/documentation/article?id=11136 while the newer documentation of...
View ArticleError with GenomicsDBImport input file
Hi, I am trying to run GenomicsDBImport to test my pipeline with just 2 samples. I am using the following code: gatk GenomicsDBImport \ -V $SCRATCH/active/memtest2/ SRR112728.raw.snps.indels.g.vcf \ -V...
View ArticleHaplotypeCallerSpark stack overflow
Dear colleagues All my attempts to use GATK HaplotypeCallerSpark with the option --spark-master local[*] fail because of stack overflow error with a similar error message as in...
View ArticleGATK v4.1.0.0 ValidateVariants, gVCF mode, error; non in v4.0.11.0
GATK v4.0.11.0 & v4.1.0.0, linux server, bash Hi, I was running the following codes ${GATK4} --java-options '-Xmx10g -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:ConcGCThreads=1...
View ArticleAllele Depth (AD) is lower than expected
The problem: You're trying to evaluate the support for a particular call, but the numbers in the DP (total depth) and AD (allele depth) fields aren't making any sense. For example, the sum of all the...
View Articleunderstand HaplotypeCaller output vcf format
Hi there, I am using GATK4.1.0.0 version on germline pair-end illumina WGS data with following command: ``` gatk4.1.0.0 --java-options '-Xmx5G' HaplotypeCaller -R...
View ArticleExcessHet filtering in cohorts with family members
This post mentions that the first step in Best Practice VQSR filtering involves hard filtering on ExcessHet. The post also states that "ExcessHet filtering applies only to callsets with a large number...
View ArticleVariantFiltration: how to filter samples where less then 95% of reads agree...
I've been looking over the documentation for VariantFilteration and jexl...
View ArticleSample Naming Scheme for PostprocessGermlineCNVCalls
GATK Version - 4.1.0.0 on GATK4 Docker I am running the PostprocessGermlineCNVCalls utility using 17 interval shards (~25k intervals each) and 8 samples. I keep getting a key error for the sample_name....
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