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GATK best practices workflow Pipeline summary

SnakeMake workflow for Human Germline short variants (SNP+INDEL)

1. Reference genome related files and GTAK budnle files (GATK)
2. VEP Variarition annotation files (VEP)

1. Adapter trimming (Fastp)
2. Aligner (BWA mem2)
3. Mark duplicates (samblaster)
4. Generates recalibration table for Base Quality Score Recalibration (BaseRecalibrator)
5. Apply base quality score recalibration (ApplyBQSR)

1. Fastp report (MultiQC)
2. Alignment report (MultiQC)

1. Call germline SNPs and indels via local re-assembly of haplotypes (HaplotypeCaller)
2. Import VCFs to GenomicsDB (GenomicsDBImport)
3. Perform joint genotyping on one or more samples pre-called with HaplotypeCaller (GenotypeGVCFs)

1. Select a SNP or INDEL of variants from a VCF file (SelectVariants)
2. Build a recalibration model to score variant quality for filtering purposes (VariantRecalibrator)
3. Apply a score cutoff to filter variants based on a recalibration table (ApplyVQSR)
4. Merge all the VCF files (Picard)

Annotate variant calls with VEP (VEP)

├── config
│   ├── captured_regions.bed
│   ├── config.yaml
│   └── samples.tsv
├── dag.svg
├── logs
│   ├── annotate
│   ├── call
│   ├── filter
│   ├── prepare
│   ├── qc
│   ├── ref
│   └── trim
├── raw
│   ├── SRR24443168.fastq.gz
│   └── SRR24443169.fastq.gz
├── README.md
├── report
│   ├── fastp_multiqc_data
│   ├── fastp_multiqc.html
│   ├── prepare_multiqc_data
│   ├── prepare_multiqc.html
│   └── vep_report.html
├── results
│   ├── called
│   ├── filtered
│   ├── prepared
│   ├── trimmed
│   └── vep_annotated.vcf.gz
├── workflow
│   ├── envs
│   ├── report
│   ├── rules
│   ├── schemas
│   ├── scripts
│   └── Snakefile