Getting started with GATK is easier on Terra
GATK has always been kind of a beast to get started with -- command-line program, many different tools under the hood, complex algorithms, multi-step pipelines, scale of computational resources...
View ArticleMethylationTypeCaller for analyzing Bisulphite sequencing data
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View ArticleHigh Ti/Tv values
Hi there. We are trying to run VariantRecalibrator (SNP mode) on a set of ~4000 cattle WGS samples (Bos Taurus & Bos Indicus). We are using GATK v3.8. We seem to be getting quite high Ti/Tv values...
View ArticleProblem with a BED file and the flag -alleles (HaplotypeCaller)
I'm trying to pass the flag -gt_mode GENOTYPE_GIVEN_ALLELES by giving a list of SNP in a BED file. This BED file has 4 columns (chromosome, initial position, final position, allele, allele). However...
View ArticleM2 and GDBI for PON: [E::vcf_parse_format] Invalid character '.' in 'AF'...
GATK 4.1.1.0, local linux server Hi, I ran some WES normal samples: ${gatk} Mutect2 \ -R ${hg38} \ -I "${sample}.bam" \ -O "${sample}.vcf.gz" \ -L ${interval} \ -ip 5 \ --max-mnp-distance 0 and then...
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Missing variant using RNA-seq best practices
Hi, I am doing variant calling on RNA-seq data processed according to the RNA-seq best practices guide published on this site. In general I am satisfied with the results, but I am missing one variant...
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What is a VCF and how should I interpret it?
This document describes "regular" VCF files produced for GERMLINE calls. For information on the special kind of VCF called gVCF, produced by HaplotypeCaller in -ERC GVCF mode, please see this companion...
View ArticleHow do we view the specific annotations in each annotation group
Hi there, when using GATK4 you can provide an annotation group argument to tools such as halpotype caller. I am having difficulties finding out how to figure out what annotations belong to each group....
View ArticleMutect2 speed varies greatly fold across regions
Hi, I am trying to run Mutect2 on WES data on a cluster where I need to use 24 cores simultaneously. To parallelize this I used SplitIntervals to create 24 equal intervals and run a single instance of...
View ArticleCan Base Quality Score Recalibration (BQSR) result in mixed phred scores?
I have .bam files with phred scores ranging from 1-66. It seems to be a mix of Phred + 33 and Phred + 64 . I was wondering if it is possible that this could have happened int the BQSR in the Picard...
View Article"Failed to create reader" error in GenomicsDBImport
I ran GenomicsDBImport and got the error below. Perhaps it is worth noting that I'm running this in Nextflow (nextflow.io), because I didn't have this problem outside of Nextflow. 15:54:24.801 INFO...
View ArticleVQSR with two data sets
Hi, I would like to Build the SNP recalibration model with two data sets. 1- SNPs derived from WGS and filtered 2- SNps derived from SNP array chip data The problem that I have is that the SNPs from...
View ArticleErrors in Mutect2 AD, F1R2 and F2R1 counts
Hello GATK team, We are using GATK 4.0.10.1, and we noticed error in mutect2 ALT/REF count, that we cannot explain. Some variant will be reported with coverage from forward and reverse read were there...
View ArticleWhat is the correct syntax for intervals for multiple chromosomes using the...
Hi, I've previously defined intervals using the -L flag with HaplotypeCaller for say -L chr1 for chromosome 1, and -L chr1 and -L chr2 for chromosome 1 and chromosome 2. What is the syntax for putting...
View ArticleGenomicsDBImport or CombineGvcfs on WGS dataset
Hi, I'm currently setting up a pipeline for my group to make master-vcf's (vcf's containing all our samples) per species we work with. Per (non-model)species we have samples sizes ranging from 50 to...
View ArticleHow can i do alignment to my fastq data?
I got several fastq data, and i just read some pipeline you guys released here. And i don't which way is better to do alignment. One way should be like this: i should convert the fastq data into ubam,...
View ArticleSelectVariants no suitable codecs found
Hi, I am trying to run SelectVariants (gatk 4.1.2.0) on the vcf output of FilterMutectCalls. I get the following error: org.broadinstitute.hellbender.exceptions.UserException$NoSuitableCodecs: Cannot...
View ArticleSNP calling for Cell lines - how does the ploidy affect HC
Hi all, I am calling SNPs in various immortalised cell lines, which are known to be very instable - hence the ploidy is not known. Generally it should be diploid. So my question is - what can happen if...
View ArticleLiftoverVCF SVs
Hi, I'm trying to use LiftoverVcf for structural gnomad variants hg19 to h38. I get MismatchedRefAllele in the rejectVCF files, as well as output messages that look like this: " failed to match chain 2...
View ArticleThe parameter --model of DetermineGermlineContigPloidy when use CASE mode
When I use DetermineGermlineContigPloidy about CASE mode: ``` gatk DetermineGermlineContigPloidy \ --model a_valid_ploidy_model_dir --input normal_1.counts.hdf5 \ --input normal_2.counts.hdf5 \ ... \...
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