Denovo & recessif mutation selection with variant_tools

gistfile1.txt

#!/bin/bash 

pwd 
MAMAN="maman.vcf.gz"  
PAPA="pere.vcf.gz"  
ENFANT="enfant.vcf.gz" 
DP_MAX=50 
EXAC_AF=0.001

# initialize vtools prj 
vtools init myprj 

# set vtools database path 
vtools admin --set_runtime_option='local_resource=/BIG_SPACE/sschutz/vtools'

# Import trio files  
vtools import $MAMAN --sample_name maman --var_info DP,AF --build hg19 
vtools import $PAPA --sample_name papa --geno_info DP,AF --var_info DP,AF --build hg19 
vtools import $ENFANT --sample_name enfant --geno_info DP,AF --var_info DP,AF --build hg19 

# Remove low depth 
vtools select variant "DP >= $DP_MAX" -t clean 

# Create tables for each samples  
vtools select clean --samples "sample_name =='maman'" -t maman
vtools select clean --samples "sample_name =='papa'" -t papa
vtools select clean --samples "sample_name =='enfant'" -t enfant

# Create denovo table 
vtools compare --expression "denovo = enfant - maman - papa"

# Create common table with common variant
vtools compare --expression "common = enfant & papa & maman"

# Select recessif mutation . ( homozygote for child , hetero for parent )
vtools select common "genotype('enfant') == 2 and genotype('maman')!=2 and genotype('papa')!=2" -t hetero

# Annotation 
vtools use refGene 
vtools use dbNSFP
vtools use dbSNP 

vtools select denovo "dbNSFP.ExAC_AF < 0.01" -o chr pos ref alt name2 MutationTaster_pred FATHMM_pred Polyphen2_HVAR_pred MetaSVM_pred MetaLR_pred "genotype()" > denovo_low_AF.tsv
vtools select hetero "dbNSFP.ExAC_AF < 0.01" -o chr pos ref alt name2 MutationTaster_pred FATHMM_pred Polyphen2_HVAR_pred MetaSVM_pred MetaLR_pred "genotype()" > hetero_low_AF.tsv

vtools select denovo  "clinvar_clnsig is not NULL" -o chr pos ref alt name2 MutationTaster_pred FATHMM_pred Polyphen2_HVAR_pred MetaSVM_pred MetaLR_pred "genotype()" > denovo_clinvar.tsv
vtools select hetero  "clinvar_clnsig is not NULL" -o chr pos ref alt name2 MutationTaster_pred FATHMM_pred Polyphen2_HVAR_pred MetaSVM_pred MetaLR_pred "genotype()" > hetero_clinvar.tsv

vtools select denovo  "MutationTaster_pred=='D' and FATHMM_pred=='D'" -o chr pos ref alt name2 MutationTaster_pred FATHMM_pred Polyphen2_HVAR_pred MetaSVM_pred MetaLR_pred "genotype()">denovo_D.tsv
vtools select hetero  "MutationTaster_pred=='D' and FATHMM_pred=='D'" -o chr pos ref alt name2 MutationTaster_pred FATHMM_pred Polyphen2_HVAR_pred MetaSVM_pred MetaLR_pred "genotype()">hetero_D.tsv