Cancer Genomics Data Analysis Exercise

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1. download human genome rference sequence:
   curl "http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.X.fa.gz" --output Homo_sapiens.GRCh38.dna.chromosome.X.fa.gz
2. download samples
3. run script
   scripts/read_dept_plot.sh <ref sequence> <tumor reads 1> <tumor reads 2> <wild reads 1> <wild reads 2>

scripts/read_dept_plot.sh:

1. create index for reference sequence
   samtools faidx
2. create bwa index for reference sequence
   bwa index
3. map tumor samples and wild type samples to reference sequence
   bwa mem
4. convert sam files to bam files
   samtools view -S -b
5. sort bam files
   samtools sort
6. index bam msorted files
   samtools index
7. generate read-dept statistics of mapped samples
   samtools depth
8. run R script to plot read-dept plot
   Rscript ./amcr.R