/KLA_Whole_exome_sequence

WES pipeline for rerun a KLA reserarch paper

Primary LanguageShell

Kaposiform Lymphangiomatosis Whole Exome s equence Analysis pipeline

WES pipeline for rerun a Kaposiform Lymphangiomatosis reserarch paper :

A Somatic Activating NRAS Variant Associated with Kaposiform Lymphangiomatosis

the source code was refactor from the supplementary file

Setup

git clone https://github.com/whuang022nccu/KLA_Whole_exome_sequence

and change your PICARD , BWA and GATK paths :

  • picard_jar_path="your_path_to/picard-2.8.3.jar"
  • bwa_path='your_path_to/bwa-0.7.15'
  • gatk_path='your_path_to/gatk-4.0.12.0/gatk'
  • GenomeAnalysisTK_jar_path="your_path_to/GenomeAnalysisTK.jar"

and the data related :

  • ref_genome_path='your_path_to/Homo_sapiens_assembly38.fasta'
  • S04380110_Covered='your_path_to/S04380110_Covered.bed'
  • dbsnp_138_hg38_vcf='your_path_to/dbsnp_138.hg38.vcf.gz'
  • Mills_and_1000G_gold_standard_indels_h g38_vcf='your_path_to/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
  • af_only_gnomad_vcf_path="your_path_to/af-only-gnomad.hg38.vcf.gz"
  • S_1000g_pon_hg38_vcf="your_path_to/1000g_pon.hg38.vcf.gz"

Useage

change the sample path and sample ID :

  • sample_ID="your-ID"
  • sample_path="your/path"

move your raw fastq data in your/path/raw

and run :

./wes_hg38_kla.sh