136    ◾    Bioinformatics

The following bash script downloads a standard human SNPs and InDels VCF files with

their index files in the “refvcf” subdirectory and then it performs the two steps of BQSR.

Notice that for BaseRecalibrator tool, the known variant files are provided in “--known-

sites” option. The outputs of the base recalibration are stored in “applyBQSR” subdirectory.

mkdir refvcf

cd refvcf

wget https://storage.googleapis.com/genomics-public-data/

resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.

vcf.gz

wget https://storage.googleapis.com/genomics-public-data/

resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.

vcf.gz.tbi

wget https://storage.googleapis.com/genomics-public-data/

resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.

gz

wget https://storage.googleapis.com/genomics-public-data/

resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.

gz.tbi

cd ..

##B- Build the BQSR model

#------------------------

mkdir BQSR

cd RG

ref=$(ls ../refgenome/*.fasta)

for i in $(ls *.bam|rev|cut -c 5-|rev);

do

~/software/gatk-4.2.3.0/gatk --java-options \

-Xmx4g BaseRecalibrator \

-I ${i}.bam \

-R ${ref} \

--known-sites ../refvcf/1000G_phase1.snps.high_confidence.

hg38.vcf.gz \

--known-sites ../refvcf/Homo_sapiens_assembly38.known_

indels.vcf.gz \

-O ../BQSR/${i}.table

done

cd ..

##C- Apply the model to adjust the base quality scores

#----------------------------------------------------

mkdir applyBQSR

cd RG

ref=$(ls ../refgenome/*.fasta)

for i in $(ls *.bam|rev|cut -c 5-|rev);

do

~/software/gatk-4.2.3.0/gatk \

--java-options \