Questions tagged [gatk]
Genome Analysis Toolkit. Popular open-source bioinformatics suite to call variants from second-generation sequencing data.
47
questions
1
vote
0
answers
35
views
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/...
0
votes
0
answers
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 ...
- 135
3
votes
0
answers
62
views
Funcotator reference file error in GATK4
I am using a function called Funcotator (here) in GATK4. The code I am trying to run is:
...
- 135
6
votes
1
answer
134
views
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 ...
- 8,111
1
vote
1
answer
99
views
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 ...
- 200
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 ...
- 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?
...
- 1,607
-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/...
- 1,607
1
vote
0
answers
62
views
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 ...
- 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:
...
- 21
0
votes
0
answers
39
views
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&...
- 1
0
votes
0
answers
34
views
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 ...
- 1,723
0
votes
1
answer
60
views
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 ...
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....
- 11
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
...
- 161
0
votes
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 ...
- 101
2
votes
1
answer
77
views
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 ...
- 21
0
votes
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:
...
- 29
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 ...
- 139
0
votes
0
answers
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 ...
- 76
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):
...
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
...
- 140
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 ...
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 ...
- 183
0
votes
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 ...
- 314
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 ...
- 2,644
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 ...
- 314
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. ...
- 314
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:
...
- 61
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
...
- 11
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 ...
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?
...
- 29
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), ...
- 1,607
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 ...
- 206
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 ...
- 1,234
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 ...
- 510
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 ...
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
...
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 ...
- 399
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 :...
- 11
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:
...
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 ...
- 2,349
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 ...
- 510
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, ...
- 445
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:
...
- 1,723
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 ...
- 767
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. ...
- 303