Applied Genomics Final Project

NYU Spring 2021

1. Download_data.sh

   a. Download fastq files from SRA run selector

2. Fastqc.sh

   a. Run and review QC results

3. ref_genome.sh

   a. Download reference genome zip (https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies#hg19)

   i. Manually uploaded from local to ...Final_Project/data/genome directory

   ii. Unzip: in command line tar -zxvf chromFa.tar.gz

   iii. Concatenate: in command line cat chr*.fa > hg19.fa

   b. Index

4. Align.sh

   a. Using bwa

   b. Output of seq alignment is a sam file

5. Sam_to_bam.sh

   a. Sort the sam file by coordinate and convert to bam (bam = binary version)

   b. Deleted the sam files

6. Dedup.sh

   a. Mark (PCR) duplicates using Picard/GATK

7. Readgroups.sh

   a. Add readgroups

8. Sequence dict from ref genome & index bam files

   a. Indexing

   i. Create Sequence Dictionary from Reference Genome

   ii. Index ref

   iii. Index dedup.bam

9. VARIANT CALLING

   a. GATK.sh

   i. Haplotype caller

   b. GATK_INDEL_SNP.sh

   i. Separate indels and SNPs

   c. GATK_var_filt.sh

   i. Filtering

   d. snpEff.sh

   i. ANNOTATION