Introduction

Serpentine is, so far, a collection of rules and workflows for NGS data processing. It is in development.

Installation

The easiest way to get serpentine is to clone the repository.

git clone https://github.com/NCI-CCR-GB/serpentine.git

Contributing

To contribute to the project, you can:

1. File a new issue
2. Fork the repository, make changes, and then make a pull request.

If you have questions, file a new issue and label as a question or email me.

Roadmap (to be updated)

1. Implement germline workflow(s) for DNA
   • bwa-freebayes
     • bwa alignment (100%)
     • GATK processing (80%)
     • freebayes calling (multisample)
     • GATK VQSR
   • bwa-HaplotypeCaller
     • bwa alignment (100%)
     • GATK processing (80%)
     • freebayes calling (multisample)
     • GATK VQSR
   • Novoalign-HaplotypeCaller
     • novoalign alignment
     • GATK processing (80%)
     • freebayes calling (multisample)
     • GATK VQSR
   • reporting
     • fastqc (100%)
     • duplicate metrics (100%)
     • recalibration tables (100%)
     • alignment stats
2. Implement RNA-seq workflow
3. Implement Somatic workflows

Conventions

• Sample names cannot have "/" or "." in them
• fastq files end in ".fastq.gz"

output locations

$ tree [analysis_dir]

STUDY/
`-- variant
    `-- human_g1k_v37.bwamem
        |-- freebayes_all.vcf.gz
        |-- freebayes_all.vcf.gz.tbi
        |-- unifieldgenotyper_all.vcf.gz
        |-- unifieldgenotyper_all.vcf.gz.tbi
        `-- unifieldgenotyper_all.vcf.idx
SUBJECT/
|-- NA12878
|   `-- NA12878_DNA
|       `-- human_g1k_v37.bwamem
|           |-- bam
|           |   |-- NA12878_DNA.final.bai
|           |   |-- NA12878_DNA.final.bam
|           |   |-- NA12878_DNA.final.bam.bai
|           |   `-- NA12878_DNA.final.bam.tdf
|           |-- freebayes
|           |   |-- NA12878_DNA.freebayes.vcf.gz
|           |   `-- NA12878_DNA.freebayes.vcf.gz.tbi
|           |-- germline_compare
|           |-- haplotypecaller
|           |   |-- NA12878_DNA.haplotypecaller.vcf.gz
|           |   |-- NA12878_DNA.haplotypecaller.vcf.gz.tbi
|           |   `-- NA12878_DNA.haplotypecaller.vcf.idx
|           |-- mutect
|           |   |-- NA12878_DNA_vs_NA12891_DNA.mutect.call_stats.txt
|           |   |-- NA12878_DNA_vs_NA12891_DNA.mutect.coverage.wig.txt
|           |   |-- NA12878_DNA_vs_NA12892_DNA.mutect.call_stats.txt
|           |   `-- NA12878_DNA_vs_NA12892_DNA.mutect.coverage.wig.txt
|           |-- pindel
|           |   |-- NA12878_DNA.pindel.txt
|           |   |-- NA12878_DNA.pindel.vcf.gz
|           |   |-- NA12878_DNA.pindel.vcf.gz.tbi
|           |   |-- NA12878_DNA.pindel_BP
|           |   |-- NA12878_DNA.pindel_CloseEndMapped
|           |   |-- NA12878_DNA.pindel_D
|           |   |-- NA12878_DNA.pindel_INT_final
|           |   |-- NA12878_DNA.pindel_INV
|           |   |-- NA12878_DNA.pindel_LI
|           |   |-- NA12878_DNA.pindel_RP
|           |   |-- NA12878_DNA.pindel_SI
|           |   `-- NA12878_DNA.pindel_TD
|           |-- platypus
|           |   |-- NA12878_DNA.platypus.log
|           |   |-- NA12878_DNA.platypus.vcf.gz
|           |   `-- NA12878_DNA.platypus.vcf.gz.tbi
|           |-- qc
|           |   |-- NA12878_DNA.final.bam.base_distribution_by_cycle.pdf
|           |   |-- NA12878_DNA.final.bam.base_distribution_by_cycle_metrics
|           |   |-- NA12878_DNA.final.bam.insert_size_Histogram.pdf
|           |   |-- NA12878_DNA.final.bam.insert_size_metrics
|           |   |-- NA12878_DNA.final.bam.quality_by_cycle.pdf
|           |   |-- NA12878_DNA.final.bam.quality_by_cycle_metrics
|           |   |-- NA12878_DNA.final.bam.quality_distribution.pdf
|           |   |-- NA12878_DNA.final.bam.quality_distribution_metrics
|           |   `-- NA12878_DNA.final.bam.summetrics
|           |-- strelka
|           |   |-- NA12878_DNA_vs_NA12891_DNA.strelka.indels.vcf.gz
|           |   |-- NA12878_DNA_vs_NA12891_DNA.strelka.indels.vcf.gz.tbi
|           |   |-- NA12878_DNA_vs_NA12891_DNA.strelka.snvs.vcf.gz
|           |   |-- NA12878_DNA_vs_NA12891_DNA.strelka.snvs.vcf.gz.tbi
|           |   |-- NA12878_DNA_vs_NA12892_DNA.strelka.indels.vcf.gz
|           |   |-- NA12878_DNA_vs_NA12892_DNA.strelka.indels.vcf.gz.tbi
|           |   |-- NA12878_DNA_vs_NA12892_DNA.strelka.snvs.vcf.gz
|           |   `-- NA12878_DNA_vs_NA12892_DNA.strelka.snvs.vcf.gz.tbi
|           `-- unifieldgenotyper
|               |-- NA12878_DNA.unifieldgenotyper.vcf.gz
|               |-- NA12878_DNA.unifieldgenotyper.vcf.gz.tbi
|               `-- NA12878_DNA.unifieldgenotyper.vcf.idx
..