grch37-lite in Call Somatic Mutations WGS
TARGET WGS data was aligned to GRCH37-lite. Internally, GP has aligned to Hg19. Is there a easy way to merge the two together without having to realign the TARGET data (and take up a lot of space...
View ArticleAnnotation for Germline mutation list
I have identified germline mutations with GATK tools, and got final germline mutation list with GATK GenotypeGVCFs in vcf format. I tried to annotate this vcf file with Oncotator, but got error...
View ArticleVariantsToBinaryPed Throwing IndexOutofBoundsException
Hi All, I am trying to use the GATK v3.7 VariantsToBinaryPed on my multi-sample VCF file to create PLINK files. However it is throwing an error, the stack trace is shown below... ##### ERROR -- #####...
View ArticleHTSJDK SamLocusIterator / SamReader pass bamindex file
Hello, I don't know if it's the right place to ask this question but I'm developing some small stuff with the HTSJDK package and need to somehow tell SamLocusIterator/SamReaderFactory where it can find...
View ArticlePiccard tools error using CollectRnaSeqMetrics
Hi, I am attempting to use CollectRnaSeqMetrics from picard tools on my BAM files but I am not being successful with it for some reason. Below is the code that I am using: java -jar...
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 ArticleNo plots produced by AnalyzeCovariates GATK4-Alpha
I'm using GATK4-Alpha AnalyzeCovariates java -Xmx80G -jar $GATK AnalyzeCovariates -before recal.table -after after_recal.table -plots recal_plots.pdf The tool appears to finish however I then get an...
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 Article0" in the --input_prior documentation for the HaplotypeCaller?">Should it say "AC>0" in the --input_prior documentation for the HaplotypeCaller?
In the documentation of the --input_prior argument of the HaplotypeCaller...
View ArticleMutect2 with contamination estimates
Hi GATK How many sites does ContEst need to get an accurate answer? A couple of my samples give me results like this: name population population_fit contamination confidence_interval_95_width...
View ArticleArchived GATK 3.6
Where can I find the jar file for GATK version 3.6? Or when will it be added to the archive?
View ArticleQuestions about the RNAseq variant discovery workflow
This discussion was created from comments split from: Calling variants in RNAseq.
View ArticleRNAseq Library to SNP Call using GATK
Hi , I am working on SNP detection on multiple pair end RNAseq library: after indel realignment, I want perform base quality score recalibration by using these two steps, I do not have any information...
View ArticleMNP detection using ReadBackedPhasing
GATK team, I have used HaplotypeCaller to call variations in the exome data, performing joint calling on the samples. Then, ReadBackedPhasing was running on each sample individually with...
View ArticleMarkduplicates for a mixer of single end reads and pair end reads
We have sequenced the same library twice. One for pair-end and another one for single-end. I have to remove PCR duplicates together since they are the same library. Can Picard handle this? Or is there...
View Articlevariant calling for cancer cell lines
We want to genotype one of cancer cell lines studies in the lab. Are there any concerns or recommendations specifically for cancer cell lines? Or GATK best practice is enough.
View ArticleClik here to view.
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 ArticleSelectVariants JEXL expression not working as intended
Hello, I am trying to select all variants that are homozygous/polymorphic in either of two samples in my multisample vcf file. For example, Sample1 might be T/T (hom reference) while sample2 might be...
View ArticleHow to split a paired-end FASTQ file into two separate FASTQ files (forward...
I have to analyse a paired-end DNA-seq read that are in an unusual format: both pair-end reads are joined in one FASTQ. I already obtained this file by reverting from BAM file to FASTQ. So, I need to...
View ArticleError: Unable to access jarfile picard-tools-2.2.1/picard.jarError: Unable to...
hi, I can't find the solution of this error: Error: Unable to access jarfile picard-tools-2.2.1/picard.jar Could you help me? Thank you, Matias
View Article