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Questions tagged [gatk]

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

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Replicating VCF Filtering & Trait-Based SNP Extraction Workflow

I'm new to handling SNP genotyping data in VCF format. My goal is to identify significant SNPs linked to a specific trait (like "height") for specific samples in a multi-sample VCF file. My ...
web's user avatar
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1 vote
1 answer
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Problem while mapping reads to mtDNA (SortSam)

I am trying to map MiSeq reads to a reference genome and extract mutations using MToolBox, which implements gsnap, GATK, Picard, and other tools. When running the tool with example data, there were no ...
uri's user avatar
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0 answers
37 views

Using GATK4.2 to create .idx using IndexFeatureFile for multiple vcf files

I have used GATK script : gatk IndexFeatureFile --input sampleid_hc.g.vcf to create .idx files for individual vcf files. However I am trying to create a loop and ...
user20179's user avatar
2 votes
1 answer
85 views

How do I quantify a specific somatic variant?

I'm working with targeted Illumina sequencing data generated with DNA from diseased and healthy tissue (this is an age-related disease and is not cancer/neoplastic). My hypothesis is that the diseased ...
Nereus's user avatar
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1 answer
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How to adjust cutoffs in Mutect2

I'm currently performing some initial analyses on targeted Illumina sequencing data generated with DNA from diseased tissue. My hypothesis is that one particular gene might contain somatic mutations ...
Nereus's user avatar
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1 vote
0 answers
44 views

java.lang.ArrayIndexOutOfBoundsException: Index 86 out of bounds for length 86

I use the next versions: gatk 4.4.0.0 minimap2 2.26-r1175 samtools 1.19 I have a fastq file. And try to implement gatk MergeBamAlignment to generate a new ...
Shwarz's user avatar
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0 answers
63 views

ERROR IN FUNCOTATOR: [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)

I ran the "funcotator" step from the GATK somatic short variant discovery (snvs + indels) pipeline and used the output of filtermutectcalls as input, but ...
Rita Soares's user avatar
1 vote
2 answers
91 views

How to run a GATK Docker Image with local files?

I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command: ...
rimo's user avatar
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1 vote
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I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header

My objective is to take a g.vcf.gz file and from 25-30 unmapped contigs with titles like "NW_020192317.1", I want to make a subset of ~10k variants from each of the unmapped contigs and make ...
Lauren Sabo's user avatar
4 votes
0 answers
85 views

MergeBamAlignment error

I doing the alignment of samples following the GATK pipeline, and doing the MergeBamAlignment,like this: ...
Rita Soares's user avatar
0 votes
1 answer
119 views

A bash script for running on a bunch of bam files

I have some bam files in this directory /data/Continuum/WES/results/ I want to run GATK mutation calling over bam files I ...
Zizogolu's user avatar
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2 votes
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55 views

Importing local files to a GATK docker image

I have pulled GATK docker on my computer but when running a GATK command, can not locate my input file My OS version ...
Zizogolu's user avatar
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1 vote
0 answers
17 views

GenomicsDB and recalibration recommended for cohort of mixed exome (GATK)

We have a cohort of around 3k exomes, most of them from different capture kits, such as Agilent v6, v8, Nextera, Twist, Clinical Research exome and many others. Right now we are creating genome db on ...
Karthik Nair's user avatar
1 vote
1 answer
256 views

Getting VCF file that contain common SNPs from 6 VCF file using isec

I have 6 VCF files, where I would like to obtain the SNPs that are common (by position) in all the 6 files. I have tried this command ...
Mohamed Samir's user avatar
2 votes
1 answer
64 views

WES variant calling with DNBSEQ-T7: technical quality assessment

I recently received whole exome sequencing samples that were sequenced on an MGI sequencing instrument, DNBSEQ-T7. I am interested in somatic variant-calling on the paired tumor-normal samples. As ...
kane9530's user avatar
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1 answer
157 views

GATK SplitIntervals: A USER ERROR has occurred: but no positional argument is defined for this tool

I am trying to create a GATK g CNV pipeline and I need to make shards before running the GermlineCNVCaller therefore, I believe I need to use ...
Indira's user avatar
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2 votes
1 answer
207 views

Singularity & GATK 4.4.0.0. CreateSequenceDictionary

I ran the following code in bash (I added print statements for ease): ...
Indira's user avatar
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-1 votes
1 answer
72 views

GATK g CNV code Aborts Before Running Main Code

I have been struggling to get the code I wrote for running GATK g CNV on my Linux machine (Steps Here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152 ) to work. Specifically it seems ...
Indira's user avatar
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2 votes
2 answers
255 views

What should GC coverage bias plot of exome data look like?

I want to see if there is any GC coverage bias in some paired-end Illumina human exome data. Update This is for a variant calling project. I used the ...
Dandelion's user avatar
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2 votes
1 answer
119 views

Is it common to get different number of SNVs+Indels across samples from vcf files generated using GATK and DRAGEN (counts are higher for GATK)?

We have 2 vcf (Whole Exome Sequencing (WES) data; germline samples) files (e.g., vcf_1 and vcf_2). vcf_1 was generated (Ref. genome: hg38) using the GATK pipeline for 250 children and their parents ...
App.vsh.io's user avatar
4 votes
0 answers
136 views

Write a bash script to run gatk, fix errors with input, and rerun until completion

I have a bam file that I want to run through GATK's SplitNCigarReads tool. Because of the way the bam file was generated, the program will often fail, with an error message stating: ...
kylep's user avatar
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1 vote
0 answers
54 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/...
Mahmood Hasan's user avatar
0 votes
0 answers
53 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 ...
Scott XU's user avatar
  • 145
3 votes
1 answer
257 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: ...
Scott XU's user avatar
  • 145
6 votes
1 answer
1k 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 ...
terdon's user avatar
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1 vote
1 answer
671 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 ...
everestial's user avatar
3 votes
2 answers
6k 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 ...
Scott XU's user avatar
  • 145
0 votes
2 answers
288 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? ...
Zizogolu's user avatar
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-4 votes
1 answer
258 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/...
Zizogolu's user avatar
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2 votes
1 answer
283 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 ...
ABG's user avatar
  • 21
2 votes
0 answers
56 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: ...
Nawar's user avatar
  • 21
0 votes
1 answer
200 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 ...
Andrew Judell's user avatar
1 vote
1 answer
273 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....
Atom's user avatar
  • 11
2 votes
2 answers
910 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 ...
Shafayet Rahat's user avatar
0 votes
1 answer
278 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 ...
wdg's user avatar
  • 101
2 votes
1 answer
84 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 ...
EMPEE's user avatar
  • 21
1 vote
1 answer
634 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: ...
Ugur Toprak's user avatar
2 votes
0 answers
50 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 ...
Sergio.pv's user avatar
  • 139
0 votes
0 answers
45 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 ...
Balan's user avatar
  • 76
2 votes
1 answer
43 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): ...
Stephanie Hoyt's user avatar
1 vote
1 answer
457 views

No MQ tags in VCF files

To call minority variants in my Mtb sequences I'm using a pipeline of ...
pgcudahy's user avatar
  • 152
1 vote
1 answer
810 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 ...
Kristian Unger's user avatar
2 votes
2 answers
1k 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 ...
BCArg's user avatar
  • 283
0 votes
1 answer
541 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 ...
Tomas Bencomo's user avatar
2 votes
3 answers
2k 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 ...
aechchiki's user avatar
  • 2,676
0 votes
1 answer
393 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 ...
Tomas Bencomo's user avatar
2 votes
0 answers
47 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. ...
Tomas Bencomo's user avatar
1 vote
1 answer
382 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: ...
vodka's user avatar
  • 61
1 vote
0 answers
714 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 ...
Razi's user avatar
  • 11
1 vote
1 answer
444 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 ...
Syed M. Ijlal Haider's user avatar