Does GATK4 contain the tool HaplotypeCaller? I could not find this tool in...
I have download the latest version of GATK4 from this link:https://github.com/broadinstitute/gatk After performed ./gradlew localJar and ./gradlew sparkJar, I have built the project successfully and...
View ArticleHaplotypeCaller generates diff results on different CPUs
I encountered an interesting problem: running HaplotypeCaller on different machines generates different result for 2 sites. The machines use the same input BAM file, same reference, same java...
View ArticleException in thread "main" htsjdk.samtools.SAMException: Value was put into...
I just got this while running Picard's Mark duplicates. Thanks!
View ArticleHow to calculate annotation SOR?
Hi, After reading annotation documentation, I still couldn't get calculation of SOR. Do you set R or (R + 1/R) or refRation/altRatio as value of annotation? Can you give me an example with numbers?...
View ArticleHow to use GATK with oncology panel amplicons
We have run the ACCEL-AMPLICON™ PANEL 56G (Cat. No. AL56248) from Swifft BioSciences. Those are PCR amplicons using primers that flank known cancer mutations (in order to profile their frequency in...
View ArticleHaplotypeCaller can't find variants when using GENOTYPE_GIVEN_ALLELES?
Hello, I want to call variants in some samples with the HaplotypeCaller using the GENOTYPE_GIVEN_ALLELES mode. I have used a vcf file with 2 variants for the -alleles option, and a bed file with...
View ArticleDefault value of HaplotypeCaller
Hello Everyone, I am working with gatk tool package "HaplotypeCaller" to find SNPs and Indels. I want to know what are the initial default values of HaplotypeCaller, and can I change these values...
View ArticleERROR MESSAGE of VariantsToTable
I encountered an issue when I use VariantsToTable. Thanks. command: Ref: hg19 java -Djava.io.tmpdir=$tmp \ -jar $GATK \ -T VariantsToTable \ -R $Ref \ -V $InputDir/BQSR_AutosomeFilteredSNVs.vcf \ -F...
View ArticleNew interactive support feature in GATK4
You may have heard that we've been working on a major new release of GATK that we call GATK4. As we are getting closer to the scheduled transition of GATK4 into beta status (from its current lowly...
View ArticleBD/BI tag usage
There have been a number of questions and also a blog post regarding BD/BI and their impact on file size, but less on the impact of calling. Eg see...
View ArticleWhy does GATK LeftAlignAndTrimVariants set a missing genotype to 0/0?
Hi. I appreciate many your helps. I have one vcf file (a.vcf). This file has one variant data. The data also has missing genotypes "./." because of DP=0. The variant is tri-allelic variant as below....
View Articlejava error in hmm accelerationof HaplotypeCaller, possibly a GATK bug?
Dear GATK team, running the HaplotypeCaller with GATK 3.7, I recently got a reproducable java error which can be circumvented by disabling the pairHMM acceleration of HC by adding the...
View ArticleHaplotypeCaller is taking a long time to start
Hello GATK team! I'm running HalpotypeCaller on two different bam files at the same time (193 and 804 Mb big) that are coordinate sorted and with Read Groups information. The reference (for which I...
View ArticlegenotypeGVCFs InvocationTargetException
Hi, first off I like the idea of the new Joint Genotyping method of 3.1, thanks for the hard work! My issue: I have been running HaplotypeCaller in -ERC GVCF mode as is best practice. From the output...
View ArticleVariantsToVCF - Table Codec
Hi, Dear GATK Team, I am converting a table file (generated from VariatnsToTable) to VCF by (VariatnsToVCF). My command is: java -jar /home/wuk/software/GenomeAnalysisTK.jar -T VariantsToVCF -R...
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 ArticleRemoving variants based on the FORMAT field
Hi I have been trying to remove the Variants in my Sample with a GQ lower than 20 as part of the Genotype Refinement workflow java -jar GenomeAnalysisTK.jar -T VariantFiltration -R ref.fa -V...
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DP in the VCF is different from the number of reads in the bam file after...
I have called SNPs and want to use the reads number. However, I found in the VCF file the DP is A(which will be shown in the attached file). However, in the bam file which is used for SNP calling using...
View ArticleMutect2 output filtering for germline and somatic variants
Hi, I saw already several threads on Mutect2 outputs, but nothing really answered my question. In principle very simple: I am running currently MuTect2 with just one sample (cancer vs normal), I do not...
View Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
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