Laurent

Compound_Heterozygous

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COMPOUND HETEROZYGOUS RESEARCH

WITH EXOME SEQUENCING DATA

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Louis CHAUVIERE

UMR-S 1155

14/09/2016

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####################################### ##Zip the three vcf files #bgzip .exome.snp.vcf #bgzip .exome.snp.vcf #bgzip .exome.snp.vcf #######################################

####################################### ##Index vcf files #tabix -p vcf .exome.snp.vcf.gz #tabix -p vcf .exome.snp.vcf.gz #tabix -p vcf .exome.snp.vcf.gz #######################################

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Merge vcf files

#bcftools merge .exome.snp.vcf.gz .exome.snp.vcf.gz .exome.snp.vcf.gz -o <MERGED_OUT>.vcf #######################################

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Annotate vcf file with Annovar

#perl ~/Documents/annovar/table_annovar.pl <MERGED_OUT>.vcf ~/Documents/annovar/humandb/ -buildver hg19 -out Annotes_<MERGED_OUT>.vcf -remove -protocol refGene,cytoBand,genomicSuperDups,esp6500siv2_all,1000g2014oct_all,1000g2014oct_afr,1000g2014oct_eas,1000g2014oct_eur,snp138,ljb26_all,exac03 -operation g,r,r,f,f,f,f,f,f,f,f -nastring . -vcfinput #######################################

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Options for Compound Heterozygous research

##Nonsynonymous variants : only the vcf file must be in the folder #bash synsplic.sh

##Search variants that have a good quality and a good coverage ##Search variant present in one of the two parents and heterozygous in the child #python FirstCandidatesList.py [-h] [-d] inputfile outputfile

##Search variants that are in the same exon of the same gene ##This is an optional step: but faster for the next steps #SameExon.py [-h] [-d] inputfile outputfile

##Search variants that are in the same domain #python SearchDomains.py [-h] inputfile outputfile

##Search real Compound Heterozygous variants #python CompoundHeterozygous.py [-h] [-d] inputfile outputfile #######################################################