module load bcftools/1.8
module load slivar/0.1.1
vcf=$1
ped=$2
out=$3
echo ${vcf}
echo ${ped}
echo ${out}
gnomad=/gpfs/projects/bioinfo/najeeb/playGround/slivar/gnomad-2.1.zip
js=/gpfs/projects/bioinfo/najeeb/withKhalidHussain/Families/batch5/slivar/my.js
fasta=/gpfs/data_jrnas1/ref_data/Homo_sapiens/GRCh37/Sequences/WholeGenomeSequence/GRCh37.fa
gff=/gpfs/projects/bioinfo/najeeb/refData/Homo_sapiens.GRCh37.87.gff3.gz
	slivar expr --pass-only --vcf $vcf --ped $ped\
	--out-vcf ${out}.vcf.gz\
	--js $js \
	-g $gnomad \
	--info "variant.call_rate > 0.9"\
	--trio "DN:denovo(kid, dad, mom) && hqrv(variant, INFO, 0.001)"\
	--trio "X_DN:x_denovo(kid, mom, dad) && hqrv(variant, INFO, 0.01) && (variant.CHROM == 'X' || variant.CHROM == 'chrX')"\
	--trio "uniparent_disomy:uniparent_disomy(kid, mom, dad)"\
	--trio "rec:recessive(kid, mom, dad) && hqrv(variant, INFO, 0.01)"\
	--trio "x_recessive:x_recessive(kid, mom, dad) && hqrv(variant, INFO, 0.01) && (variant.CHROM == 'X' || variant.CHROM == 'chrX')" 
slivar expr --pass-only \
	--vcf $vcf \
	--ped $ped \
	--js $js \
	-g $gnomad \
	--trio 'lenient_denovo:lenient_denovo(kid, mom, dad) && hqrv(variant, INFO, 0.005)' \
	--trio 'lenient_ar:lenient_ar(kid, mom, dad) && hqrv(variant, INFO, 0.01) && INFO.gnomad_nhomalt_controls < 4' --out-vcf ${out}_comphet.vcf.gz
	#| bcftools csq -s - --ncsq 40 -g $gff -l -f $fasta - -O u | slivar compound-hets -s lenient_denovo -s lenient_ar -p $ped --out-vcf ${out}_comphet.vcf.gz