edited README, removed course_dir variable

README.md

@@ -2,11 +2,10 @@
 
 Tufts workshop December 2019
 
-
 This repository contains instructional material for the workshop.
 
-The raw_data directory contains reads from NA12878 gene cyp on chromosome 10
+The raw_data directory contains reads from NA12878 gene cyp on chromosome 10, from 1000 genome phase 3 release
 
-The ref_data directory contains a reference sequence from hg19 chromosome 10
+The ref_data directory contains a reference sequence from GrCh38 chromosome 10
 
 The all_commands.sh file contains all the commands we will use in the workshop.

all_commands.sh

 #!/bin/bash
 
-# Set the course directory, change this if you did not clone into your home dir
-course_dir=~/intro-to-ngs
-
 # Step 1
 printf "\n----\nUse BWA to Index Reference sequence\n---\n"
 
 module load bwa/0.7.17
-bwa index $course_dir/ref_data/chr10.fa
+bwa index ref_data/chr10.fa
 
 # Step 2
 printf "\n----\nUse BWA to Align Reads\n---\n"
 
-mkdir -p $course_dir/results
+mkdir -p results
 
 bwa mem \
 -M \
 -t 2 \
 -R "@RG\tID:reads\tSM:NA12878" \
-$course_dir/ref_data/chr10.fa \
-$course_dir/raw_data/na12878_1.fq $course_dir/raw_data/na12878_2.fq  \
-> $course_dir/results/na12878.sam
-
+ref_data/chr10.fa \
+raw_data/na12878_1.fq raw_data/na12878_2.fq  \
+> results/na12878.sam
 
 # Step 3
 printf "\n----\nUse Picard to Sort SAM file\n----\n"
@@ -29,46 +25,44 @@ printf "\n----\nUse Picard to Sort SAM file\n----\n"
 module load picard/2.8.0
 
 picard SortSam \
-INPUT=$course_dir/results/na12878.sam \
-OUTPUT=$course_dir/results/na12878.srt.bam \
+INPUT=results/na12878.sam \
+OUTPUT=results/na12878.srt.bam \
 SORT_ORDER=coordinate
 
 # Step 4
 printf "\n----\nUse Picard to Mark BAM duplicates\n----\n"
 
 picard MarkDuplicates \
-INPUT=$course_dir/results/na12878.srt.bam \
-OUTPUT=$course_dir/results/na12878.srt.markdup.bam \
-METRICS_FILE=$course_dir/results/na12878.markdup.txt
+INPUT=results/na12878.srt.bam \
+OUTPUT=results/na12878.srt.markdup.bam \
+METRICS_FILE=results/na12878.markdup.txt
 
 # Step 5
 printf "\n----\nUse Picard to Build a BAM Index\n----\n"
 
 picard BuildBamIndex \
-INPUT=$course_dir/results/na12878.srt.markdup.bam 
+INPUT=results/na12878.srt.markdup.bam 
 
 
 # Step 6
 printf "\n----\nUse Samtools to Build a Reference Sequence Index\n----\n"
 
 module load samtools/1.9
-samtools faidx $course_dir/ref_data/chr10.fa
+samtools faidx ref_data/chr10.fa
 
 # Step 8
 printf "\n----\nUse Picard to Build A Reference Sequence Dictionary\n----\n"
 
 picard CreateSequenceDictionary \
-REFERENCE=$course_dir/ref_data/chr10.fa \
-OUTPUT=$course_dir/ref_data/chr10.dict
+REFERENCE=ref_data/chr10.fa \
+OUTPUT=ref_data/chr10.dict
 
-# Step 7: Use GATK to call variants
+# Step 9
 printf "\n----\nUse GATK to Call Variants on the BAM\n----\n"
 
 module load GATK/3.7
 gatk -T HaplotypeCaller \
--R $course_dir/ref_data/chr10.fa \
--I $course_dir/results/na12878.srt.markdup.bam \
--o $course_dir/results/na12878.vcf 
-
-# Bonus - run VEP!
+-R ref_data/chr10.fa \
+-I results/na12878.srt.markdup.bam \
+-o results/na12878.vcf