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学习的第一个GATK找变异流程，人的种系变异的短序列变异，包括SNP和INDEL。写了一个SnakeMake分析流程，从fastq文件到最后的vep注释后的VCF文件，关于VCF的介绍可以参考上一篇推文基因序列变异信息VCF (Variant Call Format)
流程代码在https://jihulab.com/BioQuest/smkhgs或https://github.com/BioQuestX/smkhgs
README
GATK best practices workflow Pipeline summary
SnakeMake workflow for Human Germline short variants (SNP+INDEL)
Reference
-
Reference genome related files and GTAK budnle files (GATK) -
VEP Variarition annotation files (VEP)
Prepare
-
Adapter trimming (Fastp) -
Aligner (BWA mem2) -
Mark duplicates (samblaster) -
Generates recalibration table for Base Quality Score Recalibration (BaseRecalibrator) -
Apply base quality score recalibration (ApplyBQSR)
Quality control report
-
Fastp report (MultiQC) -
Alignment report (MultiQC)
Call
-
Call germline SNPs and indels via local re-assembly of haplotypes (HaplotypeCaller) -
Import VCFs to GenomicsDB (GenomicsDBImport) -
Perform joint genotyping on one or more samples pre-called with HaplotypeCaller (GenotypeGVCFs)
Filter
-
Select a SNP or INDEL of variants from a VCF file (SelectVariants) -
Build a recalibration model to score variant quality for filtering purposes (VariantRecalibrator) -
Apply a score cutoff to filter variants based on a recalibration table (ApplyVQSR) -
Merge all the VCF files (Picard)
Annotation
Annotate variant calls with VEP (VEP)
SnakeMake Report
Outputs
.
├── 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
Directed Acyclic Graph
Reference
GATK best practices workflow: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows
GATK: https://software.broadinstitute.org/gatk/
VEP: https://www.ensembl.org/info/docs/tools/vep/index.html
fastp: https://github.com/OpenGene/fastp
BWA mem2: http://bio-bwa.sourceforge.net/
samblaster: https://github.com/GregoryFaust/samblaster
BaseRecalibrator: https://gatk.broadinstitute.org/hc/en-us/articles/13832708374939-BaseRecalibrator
ApplyBQSR: https://github.com/GregoryFaust/samblaster
HaplotypeCaller: https://gatk.broadinstitute.org/hc/en-us/articles/13832687299739-HaplotypeCaller
GenomicsDBImport: https://gatk.broadinstitute.org/hc/en-us/articles/13832686645787-GenomicsDBImport
GenotypeGVCFs: https://gatk.broadinstitute.org/hc/en-us/articles/13832766863259-GenotypeGVCFs
SelectVariants: https://gatk.broadinstitute.org/hc/en-us/articles/13832694334235-SelectVariants
VariantRecalibrator: https://gatk.broadinstitute.org/hc/en-us/articles/13832694334235-VariantRecalibrator
ApplyVQSR: https://gatk.broadinstitute.org/hc/en-us/articles/13832694334235-ApplyVQSR
Picard: https://broadinstitute.github.io/picard
MultiQC: https://multiqc.info
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