Next-Generation-Sequencing-Pipelines

St George's University of London - Genetics Centre Bioinformatics

Scripts for QC, Alignemnt, Variant Calling and Joint Genotyping of Exome Sequence Data. Following the GATK Best Practices guidelines.

• Directory/file structure:

  • Genetics_Centre_Bioinformatics/Exomes
    • ./Aligned
    • ./Unaligned
    • ./raw_FASTQ
    • ./tmp
    • ./UBAMs
    • ./VCF
    • ./FastQC
    • ./FastQC_before

• Needs the following resources to run: For more information check dependencies.py

  • FastQC
  • MultiQC
  • python2.7. These scripts have been developed and tested using python2.7. Feel free to update them.
  • bwa
  • human_g1k_v37.fasta
  • samtools
  • java
  • picard-2.815
  • gatk-4.0.4.0
  • Genome_reference_files/common_all.vcf
  • Mills_and_1000G_gold_standard.indels.hg19_modified.vcf
  • 1000G_phase1.snps.high_confidence.hg19.sites.vcf
  • BroadExACExomeIntervlas.bed (Exome Target, the this case the Broad definition)