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The following is based on a homework assignment submitted for the Applied Bioinformatics course.

0 results • updated 2.4 years ago by Istvan Albert • needs authorization

The following is based on a homework assignment submitted for the Applied Bioinformatics course.

The recipe has been updated and edited for reproducibility but otherwise kept in its original form.

Data for the analysis came from the Whole genome sequencing project of SARS-CoV-2 conducted by the California Department of Public Health. The reference genome for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome was downloaded from NCBI.

To install GATK follow the instructions here:

https://github.com/broadinstitute/gatk/releases

For this recipe we assume GATK was downloaded and stored in ~/Downloads/gatk-4.2.3.0/gatk

Also install bio with:

pip install bio --upgrade

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#
# Download and unpack gatk in a folder
#
# https://github.com/broadinstitute/gatk/releases
#
# mine is located in: ~/Downloads/gatk-4.2.3.0/gatk
#
set -uex

# Or use fastq dump
SRR=SRR15595110

fastq-dump -X 10000 --split-files $SRR

# Accesion number
ACC=NC_045512 

# Output file names.
REF=refs/$ACC.fa
DICT=refs/$ACC.dict
BAM=$SRR.bam

mkdir -p refs

# Install bio if needed.
# pip install bio --upgrade

# Get the reference
bio fetch NC_045512 -format fasta  > $REF

# Read groups are a way to TAG data with a label (RG) a sample (SM) and a library (LB) tag.
TAG="@RG\tID:$SRR\tSM:$SRR\tLB:$SRR"

# Shortcuts to files.
R1=${SRR}_1.fastq
R2=${SRR}_2.fastq

# Index the reference
bwa index $REF

# Run the alignment
bwa mem -R $TAG $REF $R1 $R2 | samtools sort > $BAM

# Index the resulting BAM file
samtools index $BAM

# Index the reference
samtools faidx $REF

# Picard won't create the dictionary file if exists.
rm -f $DICT

# Create the dictionary file.
picard CreateSequenceDictionary -REFERENCE $REF -OUTPUT $DICT

# Run GATK
~/Downloads/gatk-4.2.3.0/gatk HaplotypeCaller -R $REF -I $BAM -O variants.vcf

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