10 Variant Calling

In this step we will call the variants using HaplotypeCaller in GATK software.

module load GATK/4.0
export _JAVA_OPTIONS=-Djava.io.tmpdir=/scratch

cd ../${d6}/ 

gatk HaplotypeCaller \
        --reference ${hg19} \
        --input ../${d5}/${INPUT_FILE_NAME}_karyotype.bam \
        --output ${INPUT_FILE_NAME}_haplotype.vcf

This creates a VCF file called ${INPUT_FILE_NAME}_haplotype.vcf, containing all the variant sites the HaplotypeCaller evaluate including both SNPs and Indels.

haplotypes/
├── SRR1517848_haplotype.vcf
├── SRR1517848_haplotype.vcf.idx
├── SRR1517878_haplotype.vcf
├── SRR1517878_haplotype.vcf.idx
├── SRR1517884_haplotype.vcf
├── SRR1517884_haplotype.vcf.idx
├── SRR1517906_haplotype.vcf
├── SRR1517906_haplotype.vcf.idx
├── SRR1517991_haplotype.vcf
├── SRR1517991_haplotype.vcf.idx
├── SRR1518011_haplotype.vcf
├── SRR1518011_haplotype.vcf.idx
├── SRR1518158_haplotype.vcf
├── SRR1518158_haplotype.vcf.idx
├── SRR1518253_haplotype.vcf
└── SRR1518253_haplotype.vcf.idx