Questions tagged [gatk]

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

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1answer
31 views

No MQ tags in VCF files

To call minority variants in my Mtb sequences I'm using a pipeline of ...
0
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1answer
58 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 ...
1
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2answers
62 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 ...
0
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1answer
86 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 ...
2
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3answers
81 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 ...
0
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0answers
294 views

Using BaseRecalibrator in GATK4

GATK4's BaseRecalibrator uses a list of known variants to adjust the base quality scores in a BAM file. I would like to visualize the pre and post recalibration ...
0
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1answer
89 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 ...
2
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0answers
41 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. ...
1
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1answer
94 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: ...
1
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0answers
100 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 ...
1
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1answer
88 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 ...
1
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1answer
123 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? ...
2
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2answers
141 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), ...
4
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2answers
139 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 ...
6
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1answer
110 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 ...
1
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0answers
133 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 ...
5
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2answers
798 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 ...
3
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1answer
2k 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 ...
3
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1answer
141 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 ...
1
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0answers
55 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 :...
4
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3answers
665 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: ...
4
votes
2answers
568 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 ...
6
votes
1answer
910 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 ...
6
votes
2answers
8k 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, ...
4
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1answer
197 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: ...
5
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3answers
357 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 ...
20
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2answers
2k 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. ...