compare different variant normalization methods

compare.sh

set -eo pipefail

REF=human_g1k_v37_decoy.fasta
VCF=Mills_and_1000G_gold_standard.indels.b37.vcf.gz
VCF=/usr/local/src/gemini/test/test.mult-alts.fb.vep.vcf.gz

java -Xmx4G -jar /usr/local/src/gatk/GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants --splitMultiallelics --trimAlleles \
    -R $REF \
    --variant $VCF -o gatk.norm.vcf


vt decompose $VCF | vt normalize -r $REF - > vt.norm.vcf

python /usr/local/src/gemini/gemini/vcfutils.py $VCF $REF > gemini.norm.vcf

grep -cv '#' *.norm.vcf

# all come out sorted in this case.
for v in *.norm.vcf; do bgzip -f $v && tabix ${v}.gz; done

paste <(zless vt.norm.vcf.gz | grep -v '^#' | cut -f -5 | sort -k2,2n -k4,5) \
	  <(zless gemini.norm.vcf.gz | grep -v '^#' | cut -f -5 | sort -k2,2n -k4,5) \
   | awk '$4 != $9 || $5 != $10 || $2 != $7' | wc -l

paste <(zless gatk.norm.vcf.gz | grep -v '^#' | cut -f -5 | sort -k2,2n -k4,5) \
	  <(zless gemini.norm.vcf.gz | grep -v '^#' | cut -f -5 | sort -k2,2n -k4,5) \
   | awk '$4 != $9 || $5 != $10 || $2 != $7' | wc -l


# compare the genotype cols
paste <(zless vt.norm.vcf.gz | grep -v '^#' | sort -k2,2n -k4,5 | cut -f 9-11) \
	  <(zless gatk.norm.vcf.gz | grep -v '^#' | sort -k2,2n -k4,5 | cut -f 9-11) \
	  <(zless gemini.norm.vcf.gz | grep -v '^#' | sort -k2,2n -k4,5 | cut -f 9-11) \
   | less