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
GATK best practices workflow Pipeline summary
SnakeMake workflow for Human Germline short variants (SNP+INDEL)
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
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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原创声明:本文系作者授权腾讯云开发者社区发表,未经许可,不得转载。
如有侵权,请联系 cloudcommunity@tencent.com 删除。