View source for 2016-VAT VMT

===VMT===
 ##################################
 # Example 1: Autosomal recessive #
 ##################################
 
 vtools init VMT --force
 vtools import AR1.vcf.gz AR2.vcf.gz --format NSHI.fmt --build hg19 -j8
 vtools show tables
 vtools show samples
 vtools execute ANNOVAR geneanno
 vtools use dbNSFP.DB
 vtools use refGene
 vtools show fields
 vtools select variant "(ExAC_AF is NULL or ExAC_AF<0.0005) AND (ExAC_SAS_AF is NULL or ExAC_SAS_AF<0.0005)"  -t  ExAC0005
 vtools select ExAC0005 "CADD_phred>20 or CADD_phred is NULL" -t CADD20
 vtools select CADD20 "region_type is 'splicing' OR (mut_type is not NULL AND mut_type is not 'synonymous SNV' AND mut_type is not 'unknown')" -t ANNOVARtype
 vtools select ANNOVARtype "dbNSFP.chr is not null" --output chr pos ref alt sift_pred lrt_pred fathmm_pred mutationtaster_pred mutationassessor_pred polyphen2_hdiv_pred polyphen2_hvar_pred provean_pred MetaLR_pred MetaSVM_pred >snv.txt
 python choose_damaging_variants.py snv.txt
 vtools update ANNOVARtype --format VMT_annotation.fmt --from_file snv.txt.parsed 
 vtools select ANNOVARtype "vmt_annotation='damaging_SNV'" -t damaging                                                                                                                      
 vtools select damaging "chr=16 AND (pos>=63600000 AND pos<=79700000)" -o chr pos ref alt region_type region_name mut_type function rs_dbSNP141 ExAC_Adj_AF ExAC_SAS_AF CADD_phred FATHMM_pred LRT_pred MetaLR_pred MetaSVM_pred MutationAssessor_pred MutationTaster_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred PROVEAN_pred SIFT_pred "samples('geno_filter=GT=1')" "samples('geno_filter=GT=2')"
 vtools update damaging --from_stat "totX=#(GT)" "homX=#(hom)" --samples "sample_name='L1' OR sample_name='L2'" -j2
 vtools select damaging "totX=homX AND totX=2" -t homL1_L2
 vtools remove fields totX homX
 vtools output homL1_L2 chr pos ref alt region_type region_name mut_type function rs_dbSNP141 ExAC_Adj_AF ExAC_SAS_AF CADD_phred FATHMM_pred LRT_pred MetaLR_pred MetaSVM_pred MutationAssessor_pred MutationTaster_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred PROVEAN_pred SIFT_pred "samples('geno_filter=GT=1')" "samples('geno_filter=GT=2')"
 
 ##################################
 # Example 2: Autosomal dominant  #
 ##################################
 
 vtools import AD.vcf.gz --format NSHI.fmt --build hg19 -j8
 vtools show tables
 vtools show samples
 vtools select variant "(ExAC_AF is NULL or ExAC_AF<0.0005) AND (ExAC_NFE_AF is NULL or ExAC_NFE_AF<0.0005)"  --samples "sample_name='AD1' OR sample_name='AD2'" -t  ExAC0005_AD
 vtools select ExAC0005_AD "CADD_phred>15 or CADD_phred is NULL" -t CADD15_AD
 vtools select CADD15_AD "dbNSFP.chr is not null" --output chr pos ref alt sift_pred lrt_pred fathmm_pred mutationtaster_pred mutationassessor_pred polyphen2_hdiv_pred polyphen2_hvar_pred provean_pred MetaLR_pred MetaSVM_pred >snv.txt
 python choose_damaging_variants.py snv.txt 
 vtools update variant --format VMT_annotation.fmt --from_file snv.txt.parsed 
 vtools select CADD15_AD "vmt_annotation='damaging_SNV'" -t damaging_AD                                                                                                                      
 vtools update damaging_AD --from_stat "totX=#(GT)" "hetX=#(het)" --samples "sample_name='AD1' OR sample_name='AD2'" -j2
 vtools select damaging_AD "totX=hetX AND totX=2" -t hetAD_2
 vtools remove fields totX hetX
 vtools output hetAD_2 chr pos ref alt refGene.name2 rs_dbSNP141 ExAC_Adj_AF ExAC_SAS_AF CADD_phred FATHMM_pred LRT_pred MetaLR_pred MetaSVM_pred MutationAssessor_pred MutationTaster_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred PROVEAN_pred SIFT_pred "samples('geno_filter=GT=1')" "samples('geno_filter=GT=2')"
 
 ##################################
 #       Example 3: De Novo       #
 ##################################
 
 vtools import de_novo.vcf.gz --format NSHI.fmt --build hg19 -j8
 vtools show tables
 vtools show samples
 vtools update variant --from_stat "totX=#(GT)" "hetX=#(het)" --samples "sample_name='Son'" -j2
 vtools select variant "totX=hetX AND totX=1" -t Son_het
 vtools update Son_het --from_stat "totX=#(GT)" "wtX=#(wtGT)" --samples "sample_name='Dad' OR sample_name='Mom'" -j2
 vtools select Son_het "(totX=wtX AND totX=2) and ((ExAC_AF is NULL or ExAC_AF<0.0005) AND (ExAC_NFE_AF is NULL or ExAC_NFE_AF<0.0005))" -t deNovo
 vtools output deNovo chr pos ref alt refGene.name2 rs_dbSNP141 ExAC_Adj_AF ExAC_NFE_AF CADD_phred FATHMM_pred LRT_pred MetaLR_pred MetaSVM_pred MutationAssessor_pred MutationTaster_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred PROVEAN_pred SIFT_pred "samples('geno_filter=GT=1')" "samples('geno_filter=GT=2')"