Questions tagged [gatk]
Genome Analysis Toolkit. Popular open-source bioinformatics suite to call variants from second-generation sequencing data.
68
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Disabling / Removing / Excluding / Collapsing * Allele SNPs indicating an Overlapping Indel
I am trying to find a way to disable the reporting of Spanning or overlapping deletions (* allele) within the GATK trio genotyping pipeline or a way to properly deal with SNPs given the ...
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8
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Verify cell identity
We want to analyze from an article the sequencing data (3 rd generation) of the U2OS line, and we would like to verify if it is that cell line. I was wondering how would be the general procedure, or ...
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answer
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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 ...
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1
vote
1
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33
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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 ...
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89
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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 ...
2
votes
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answer
91
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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 ...
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84
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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 ...
- 229
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47
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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 ...
- 41
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82
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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 ...
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2
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119
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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:
...
- 1,053
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39
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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 ...
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102
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MergeBamAlignment error
I doing the alignment of samples following the GATK pipeline, and doing the MergeBamAlignment,like this:
...
- 111
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1
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148
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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 ...
- 2,232
2
votes
1
answer
65
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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
...
- 2,232
1
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answers
19
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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 ...
- 353
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313
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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
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1
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66
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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 ...
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204
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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 ...
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1
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216
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Singularity & GATK 4.4.0.0. CreateSequenceDictionary
I ran the following code in bash (I added print statements for ease):
...
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1
answer
75
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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 ...
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2
answers
300
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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 ...
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130
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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 ...
- 41
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138
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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:
...
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58
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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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54
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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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votes
1
answer
270
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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:
...
- 145
6
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1
answer
2k
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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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730
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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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answers
6k
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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 ...
- 145
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294
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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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answer
266
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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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294
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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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58
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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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231
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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
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283
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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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953
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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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304
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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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1
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86
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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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1
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675
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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
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58
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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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48
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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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43
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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
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480
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No MQ tags in VCF files
To call minority variants in my Mtb sequences I'm using a pipeline of
...
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849
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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 ...
2
votes
2
answers
1k
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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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592
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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 ...
- 364
2
votes
3
answers
2k
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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 ...
- 2,706
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403
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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 ...
- 364
2
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47
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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. ...
- 364
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1
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390
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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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