Questions tagged [gatk]
Genome Analysis Toolkit. Popular open-source bioinformatics suite to call variants from second-generation sequencing data.
31
questions
2
votes
0answers
26 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 ...
0
votes
0answers
19 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 ...
2
votes
1answer
23 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):
...
0
votes
0answers
12 views
What number to give for `-ploidy` for durum genome in GATK?
I have some genome sequencing data from durum wheat. I'm using GATK to call variants.
I got the genome sequence here: http://plants.ensembl.org/Triticum_turgidum/Info/Index Here is the reference ...
1
vote
1answer
55 views
1
vote
1answer
115 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
vote
2answers
230 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
votes
1answer
150 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
votes
3answers
136 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
votes
0answers
451 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
votes
1answer
128 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
votes
0answers
43 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
vote
1answer
139 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:
...
2
votes
0answers
169 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
...
2
votes
1answer
104 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 ...
2
votes
1answer
186 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
votes
2answers
145 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
votes
2answers
172 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
votes
1answer
116 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
vote
0answers
136 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
votes
2answers
893 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
votes
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
votes
1answer
144 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
vote
0answers
57 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
votes
3answers
886 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
638 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
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 ...
8
votes
2answers
9k 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
votes
1answer
204 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
votes
3answers
358 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
votes
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. ...
