BashGATK web helper

Helps to run your NGS analysis with BashGATK utility.

Import your configuration file example (optional)

Browse...

Path to output folder

Path to folder with FASTQ-files

Minimal allowed read length

BashGATK scripts directory

Path to conda.sh (e.g. ...miniconda3/etc/profile.d/conda.sh)

Substring marking sample name

Substring marking lane number

Platform

Choose compression level

Choose thread number

Path to reference fasta-file

Path to reference dictionary

Path to reference gff-file

UMI template 1

UMI template 2

Adapter 1 for UMI

Adapter 2 for UMI

Pixel distance for deduplication (100 or 2500)

Path to dbSNP vcf-file

Path to Millis&1000G vcf-file

Path to known indels vcf-file

Path to panel of normals vcf-file

Path to gnomad vcf-file (for Mutect2)

Path to OMIM tsv-file

Path to PhyloNGS txt-file

Path to known SpliceAI scores tsv-table

Path to target file

Path to gene masks folder

Path to variant frquencies tsv-table

Path to netrc configuration file

Genome version for SpliceAI

Minimum read depth limit for variant calling

Minimum variant allele frequency limit for variant calling (<1)

Maximum population allele frequency limit for variant calling (<1)

VarScan SNP filter 1

VarScan SNP filter 2

VarScan SNP filter 3

VarScan SNP filter 4

VarScan indel filter 1

VarScan indel filter 2

VarScan indel filter 3

VarScan indel filter 4