Questions tagged [gatk]

Genome Analysis Toolkit. Popular open-source bioinformatics suite to call variants from second-generation sequencing data.

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Weird data in VCF file

I am using GATK HaploTypeCaller for SNP calling. I have 300 samples. As far as I understand that if a sample is missing a SNP it should be denoted by ./., however, I am getting a lot of values like 0/...
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43 views

What is the best tools to find all the somatic mutations?

I am a beginner in this field. I would like to know which is the best way to get all the mutations from a certain sample. At this point, I am considering using GATK (here) and Maftools (here). I don't ...
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3 votes
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Funcotator reference file error in GATK4

I am using a function called Funcotator (here) in GATK4. The code I am trying to run is: ...
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6 votes
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Why does GATK produce both 0/1 and 1/0 genotypes in the same file? Are the two not equivalent?

I have always thought that 1/0 and 0/1 in VCF genotype fields are equivalent. And yet, GATK uses both. For example, these are ...
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1 vote
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GATK variant filtration using "SelectVariants" and use of JEXL queries

How to do variants selection in some corner cases using GATK and JEXL expressions? I am following the guidelines given in this links for variant selection for some specific cases are not as much ...
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2 votes
2 answers
223 views

How to convert a BAM file into a VCF file

I know that there is a lot of methods to do so, but most of them need to have a reference file. (For example, the GATK force me to provide a reference.) However, I think the BAM file I am working with ...
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  • 135
-1 votes
2 answers
77 views

Error in running Mutect2

I am trying to run Mutect2 on a .bam file but I get an error by Googling can not be tackled Have you seen this error? ...
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-4 votes
1 answer
73 views

Getting error in running GATK

I am trying to making a fasta doc using GATK tools but I don't know what does this error say Server2:/data2/RNASeq/Angel/gatk$ ./gatk CreateSequenceDictionary -R reference.fa Using GATK jar /data2/...
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1 vote
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MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

I have been trying to follow the GATK Best Practice Workflow for 'Data pre-processing for variant discovery' (https://gatk.broadinstitute.org/hc/en-us/articles/360035535912). This has all been run on ...
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  • 11
2 votes
0 answers
24 views

About workflow input section in DRAGEN-GATK v1 whole genome analysis script

I am trying to understand the WDL script for the DRAGEN-GATK whole genome analysis and I am faced with this input section inside the workflow definition which I really don't get: ...
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How to customise options.json and config files to run WDL workflow in a remote server (not cloud)?

I am running wdl workflow (ExomeGermlineSingleSample) with Cromwell locally. Based on here (https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/), I have set "backend": "Local&...
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When using VCF, what is the default PL value when P(genotype) is zero

The PL field represents the normalized Phred-scaled likelihoods of the genotypes considered in the variant record for each sample. It is explained in detail (in ...
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Convert VCF file to mpileup.txt

I am working on an iterative analysis that uses orthologous pipelines that require mpileup.txt files as input for a visualization step. This requires me to convert VCF files to mpileup.txt. This ...
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1 vote
1 answer
90 views

Dictionary and index of vcf for base recalibration step

I need suggestions in creating index and dictionary with vcf files. For the base recalibration step, I downloaded Homo_sapiens_assembly38.known_indels.vcf.gz from the given link: https://console.cloud....
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1 vote
1 answer
252 views

snakemake multiple parameters for multiple input and single output in snakemake. ConbineGVCFs gatk problem

I have written a rule for CombineGVCFs in gatk4. The rule is as follow ...
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1 answer
110 views

Best practice for running GATK VQSR on X chromosome

According to GATK best practice, it is recommended that different VQSR models be built for SNPs and INDELs, because the annotations for high-quality SNPs and INDELs are systematically different (if I ...
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2 votes
1 answer
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Low pass sequencing has been reported to detect common variants. How low can one go and get reliable data? Is 2X pass sequencing analysis possible?

I would like to use low pass sequencing to replace a genotyping chip to be able to detect variants up to 0.1 % allele frequency in available population data. What is the minimum depth I can opt for to ...
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  • 21
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1 answer
271 views

GATK 4.2 using IndexFeatureFile with multiple files

I am trying to use GATK IndexFeatureFile to create ".vcf.gz.tbi" file. But I have 480 files. For the pilot study I used: ...
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2 votes
0 answers
33 views

Joint variant calling of two sample sets with different coverages (~5x vs ~25x)

Let's say 50 samples were sequenced at 25x. After a while, the group realizes that the experiment is under-powered and adds 100 samples more, but at a coverage of 5x. I'm talking about WGS. The ...
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30 views

How to control/normalize for number of reads when calling SNPs using RNA-Seq?

I used the GATK pipeline to call SNPs on males and females using RNA-Seq data. But the males have a higher read count (~43-46M reads) than the females (~40-42M reads). This causes SNP counts to be ...
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2 votes
1 answer
34 views

Cromwell: can't find file ID

I am using Cromwell to test a CWL (common workflow language) implementation of the GATK somatic CNV (copy number variation) pipeline. I am currently getting the following error (full log at the end): ...
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1 vote
1 answer
210 views

No MQ tags in VCF files

To call minority variants in my Mtb sequences I'm using a pipeline of ...
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1 vote
1 answer
446 views

How to generate the json files for Cromwell workflow execution?

I am starting to use Cromwell WDL scripts for running GATK workflows on a slurm cluster. When using the paired-fastq-to-unmapped-bam script I need to define the fastq sepcifics in the appropriate json ...
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1 vote
2 answers
797 views

Marking optical or PCR duplicates with picard vs. samtools flagstat

I am trying to identify the best library prep method for noninvasive prenatal test samples, to be sequenced with Illumina Novaseq. One metric that I am evaluating is the number/ percentage of PCR or ...
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1 answer
313 views

What samples can be used for a Mutect2 Panel of Normals

I'm working on calling somatic variants from solid tissue tumors. I have one normal and one tumor sample for each patient. I plan to use Mutect2 to call somatic variants after preprocessing the data ...
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2 votes
3 answers
577 views

Get start and end coordinates per chromosome

I will use GATK for SNP calling (HaplotypeCaller). I need to feed the interval file in the command, otherwise I get errors (even though I want to use the whole genome, not a subset - btw it's not the ...
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0 votes
1 answer
259 views

Interpreting MultiQC plot of GATK BaseRecalibration data?

I'm using GATK4 to build a somatic variant calling pipeline. The pipeline uses MultiQC to aggregate quality control data, and one of the QC measures reported is base quality score recalibration from ...
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2 votes
0 answers
46 views

NA12878 equivalent for somatic variant calling [duplicate]

I'm building a somatic variant calling pipeline with snakemake. The pipeline is hosted on Github, and I'd like to use Travis CI for continuous integration testing. ...
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1 vote
1 answer
269 views

GATK 4.1.4.0 Mutect stats output

I have adapted my pipeline to the new filtering strategies implemented in gatk 4.1.4.0 and while looking at its output I noticed that the stat file generated by mutect2 has a negative number: ...
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1 vote
0 answers
402 views

vcf tools Error: Require Genotypes in VCF file in order to output Fst statistics

I want to calculate Fst by vcf tools and GATK. I did this steps: for creating gvcf: gatk HaplotypeCaller -R ref.scf.fasta -I input.bam -ERC GVCF -O out.g.vcf ...
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1 vote
1 answer
172 views

Subset a multisample VCF file

I need some help with GATK. I have a multisample vcf file containing 18125 samples. After performing PCA I have around 303 samples as outliers and I wanted to remove these samples from my multisample ...
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2 votes
1 answer
295 views

How to use -csvStats option?

I'm trying to get CSV files from snpEff -csvStats option and got stuck. I tried the code below and only got the vcf file with no contents. How can I use -csvStats option properly? ...
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2 votes
2 answers
159 views

Variant calling without matched normal sample

I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), ...
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4 votes
2 answers
250 views

Targeted NGS, up to 99% of reads have been marked as duplicates

Currently I'm performing whole analysis (pipeline from *.fastq to *.vcf) of 41 samples (targeted NGS). I rely on GATK best practices, however with some modifications. I decided to use the following ...
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6 votes
1 answer
135 views

GATK documentation for required depth to reliably call heterozygous mutation in diploid organism?

I'm looking for official GATK documentation (or a recent manuscript) that defines a general recommendation/requirement for sequencing depth to reliably call a heterozygous point mutation in a diploid ...
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2 votes
0 answers
147 views

Meaning of category in MutSigCV

I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is category. According to MutSigCV, every mutation can be divided into the following ...
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5 votes
2 answers
1k views

No variant found using GATK 4.0 HaplotypeCaller

I am doing variant calling on RNA-seq datasets from wheat which is hexaploid,the binary alignment (BAM) files were created using STAR version 2.6.0c and variant calling was done using GATK 4.0 ...
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3 votes
1 answer
3k views

Increase number of threads for GATK 4.0 HaplotypeCaller

I am using GATK version 4.0, I tried to use multiple threads for calling variants using HaplotypeCaller using following command ...
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3 votes
1 answer
155 views

Human Genome Alignment and Variant Calling Benchmarks

I am doing a project that requires bench-marking the performance of computational tools for alignment and variant calling of human genome sequencing data. In particular I would like to establish ...
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1 vote
0 answers
64 views

Normalize by counting CNV within a pool of VCF files

I’m (trying) using the GATK4 germline CNV calling pipeline. I successfully got 57 VCFs from my sample batch, called with segments (obtained by merging the contiguous intervals), like in a classic VCF :...
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4 votes
3 answers
1k views

Issues performing variant calling with GATK

I am trying to perform variant calling on a BAM file generated through STAR version STAR_2.6.0b for wheat genome using GATK haplotypecaller as follows: ...
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4 votes
2 answers
760 views

GATK CombineVariants complains the contig order in the VCF files

I have called variants on two strains of C. elegans separately. I now want to merge the VCF files into one using the following code: Create a sequence dictionary of the reference sequence Sort the ...
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6 votes
1 answer
1k views

Merge 2 VCFs from different variant callers

I am working with WES data for detection of somatic variants and I have used two variant callers because no variant caller is complete in itself. I have used GATK Haplotypecaller for small variants ...
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11 votes
2 answers
13k views

Converting VCF file to PLINK bed/bim/fam files

I am trying to find the best way to convert VCF files to PLINK binary bed/bim/fam files, but it seems like there are many varied ways to do this. (For example, using Plink 1.9 --vcf tag, bcftools, ...
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4 votes
1 answer
229 views

Where can I get the population allele frequency vcf file?

I want to use GATK to estimate cross-sample contamination for Whole Genome Sequencing data. The specific tool is ContEst and it is run with: ...
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5 votes
3 answers
368 views

Is spark widely used in bioinformatics?

I learned that GATK 4 is using Spark for parallelization. I googled around, though I am still not quite sure how spark really works and how to use it in practice. Besides GATK 4, are any other ...
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20 votes
2 answers
3k views

Single-sample vs. joint genotyping

I am trying to understand the benefits of joint genotyping and would be grateful if someone could provide an argument (ideally mathematically) that would clearly demonstrate the benefit of joint vs. ...
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