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