NGS_Data_Analysis

SRA Toolkit

https://github.com/ncbi/sra-tools/wiki

FASTQC

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

FASTP

https://github.com/OpenGene/fastp

Reference Genome for chr 1 - UCSC

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz

BWA

https://github.com/lh3/bwa

Dockerhub

https://hub.docker.com/r/broadinstitute/gatk/tags

GATK

https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels

Path to download normal and tumor data

gatk-tutorials/workshop_2002/3-somatic/bams

https://storage.googleapis.com/gatk-tutorials/workshop_2002/3-somatic/bams/normal.bam https://storage.googleapis.com/gatk-tutorials/workshop_2002/3-somatic/bams/tumor.bam

Reference genome

https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf

implementations and testing

check: https://hpc.nih.gov/training/gatk_tutorial/haplotype-caller.html