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Commands used are:
Commands used are:
*bcftools norm -f ref.fa in.vcf -O z > out.vcf.gz
*bcftools norm -f ref.fa in.vcf -O z > out.vcf.gz
*java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R ref.fa --variant in.vcf.gz -o out.vcf.gz
*java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants --trimAlleles -R ref.fa --variant in.vcf.gz -o out.vcf.gz
*vt normalize -r ref.vcf.gz -o out.vcf.gz
*vt normalize -r ref.vcf.gz -o out.vcf.gz
