Commit 8938a63d authored by Rebecca E Batorsky's avatar Rebecca E Batorsky
Browse files

first commit

parent 762cf3d7
#!/bin/bash
# Set the course directory
course_dir=/cluster/tufts/bio/tools/training/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
# Step 2
printf "\n----\nUse BWA to Align Reads\n---\n"
mkdir -p $course_dir/results
bwa mem \
-M \
-t 2 \
-R "@RG\tID:SRR098401\tSM:NA12878" \
$course_dir/ref_data/chr10.fa \
$course_dir/raw_data/na12878_1.fq $course_dir/raw_data/na12878_2.fq \
> $course_dir/results/na12878.sam
# Step 3
printf "\n----\nUse Picard to Sort SAM file\n----\n"
module load picard/2.8.0
picard SortSam \
INPUT=$course_dir/results/na12878.sam \
OUTPUT=$course_dir/results/na12878.srt.bam \
SORT_ORDER=coordinate
# Step 4
printf "\n----\nUse Picard to Mark BAM duplicates\n----\n"
picard MarkDuplicates \
INPUT=$course_dir/results/na12878.srt.bam \
OUTPUT=$course_dir/results/na12878.srt.markdup.bam \
METRICS_FILE=$course_dir/results/na12878.markdup.txt
# Step 5
printf "\n----\nUse Picard to Build a BAM Index\n----\n"
picard BuildBamIndex \
INPUT=$course_dir/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 $course_dir/ref_data/chr10.fa
# Step 8
printf "\n----\nUse Picard to Build A Reference Sequence Dictionary\n----\n"
picard CreateSequenceDictionary \
REFERENCE=$course_dir/ref_data/chr10.fa \
OUTPUT=$course_dir/ref_data/chr10.dict
# Step 7: Use GATK to call variants
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!
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@HD VN:1.5 SO:unsorted
@SQ SN:chr10 LN:135534747 M5:988c28e000e84c26d552359af1ea2e1d UR:file:/cluster/tufts/bio/tools/training/intro-to-ngs/ref_data/chr10.fa
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