Questions tagged [gatk]

Question 1

This question was also asked on Biostars I created a GTF file for HLA alleles to be used as a resource for GATK Funcotator. Running Funcotator without indexing the GTF gives this error: ...

Question 2

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 ...

Question 3

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 ...

Question 4

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 ...

Question 5

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 ...

Question 6

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 ...

Question 7

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 ...

Question 8

I ran the "funcotator" step from the GATK somatic short variant discovery (snvs + indels) pipeline and used the output of filtermutectcalls as input, but ...

Question 9

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: ...

Question 10

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 ...

Question 11

I doing the alignment of samples following the GATK pipeline, and doing the MergeBamAlignment,like this: ...

Question 12

I have some bam files in this directory /data/Continuum/WES/results/ I want to run GATK mutation calling over bam files I ...

Question 13

I have pulled GATK docker on my computer but when running a GATK command, can not locate my input file My OS version ...

Question 14

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 ...

Question 15

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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Questions tagged [gatk]

I need to index a GTF (gene transfer format) annotation file

Replicating VCF Filtering & Trait-Based SNP Extraction Workflow

Problem while mapping reads to mtDNA (SortSam)

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

How do I quantify a specific somatic variant?

How to adjust cutoffs in Mutect2

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

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

How to run a GATK Docker Image with local files?

I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header

MergeBamAlignment error

A bash script for running on a bunch of bam files

Importing local files to a GATK docker image

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

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

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