Skip to content
This repository has been archived by the owner on May 31, 2020. It is now read-only.

Latest commit

 

History

History
107 lines (60 loc) · 5.49 KB

README.md

File metadata and controls

107 lines (60 loc) · 5.49 KB
Raw

410.712

This is a project I completed for school

Multianalysis VCF Viewer allows the user to view SnpEff, ANNOVAR and ClinVar annotations at the same time, easily comparing the predictions and clinical data for each variant in a genome. To view the example data (which is the snp variants on my chromosome 22) skip to Step 3.

Requirements: Connection to the bfx3 server is required to connect to the mysql database. Each of the files used to build the database should be no more than 1GB.

Source Code: https://github.com/chall84/410.712

Quick Start: Connect to the server and go to http://bfx3.aap.jhu.edu/chall84/final/fdisplay.html

  1. Obtain the input files:

First run the analyses on YOUR_INPUT.vcf and download the appropriate ClinVar reference file. The reference genome version for your vcf will be listed in the ## comments at the top of the file. The example commands below use hg19 as the reference genome.

##SnpEff annotated VCF file

Dowload and unzip SnpEff to install (available here: http://snpeff.sourceforge.net/download.html)

Run SnpEff with this command. Match the genome version to the reference version in YOUR_INPUT.vcf:

java -Xmx4g -jar snpEff.jar GRCh37.75 YOUR_INPUT.vcf > YOUR_OUT.ann.vcf

-Xmx4g sets the maximum heap size to 4g
-jar runs the file snpEff.jar

The manual is available here: http://snpeff.sourceforge.net/SnpEff_manual.html#run

##ANNOVAR annotated VCF file

Dowload an install ANNOVAR (you must ask for a link to download here: http://download.openbioinformatics.org/annovar_download_form.php)

Download the refGene and avsnp147 databases. Make sure to select the genome version that is the reference for the input VCF

annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/
annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avsnp147 humandb/ 

    -buildver should be the reference genome used in YOUR_INPUT.vcf
    These commands put these databases in the humandb folder within ANNOVAR

Run ANNOVAR with this command:

table_annovar.pl YOUR_INPUT.vcf humandb/ -buildver hg19 -out YOUR_OUT -remove -protocol refGene,avsnp147 -operation g,f -nastring . -vcfinput -polish

-buildver should be the reference genome used in YOUR_INPUT.vcf
-remove removes the temporary files
    - protocol refGene,avsnp147 specifies the databases to be used
    - operation g,f specifes the database operations to gene and filter respectively
    -nastring . Sets the null value to a full stop
    -vcfinput specifies that the input file is a VCF
    -polish polishes the protein notation for indels

The manual is available here: http://annovar.openbioinformatics.org/en/latest/user-guide/startup/

##ClinVar VCF file

Download the ClinVar VCF. Choose the genome that matches the reference genome in YOUR_INPUT.vcf

Easy access download here: https://www.ncbi.nlm.nih.gov/genome/guide/human/ Or download from the FTP: https://www.ncbi.nlm.nih.gov/clinvar/docs/ftp_primer/

  1. Create the database:

##Run create_db.py on the bfx3 server in the folder /var/www/html/chall84/final

Create the database with this command:

./create_db.py -a YOUR_ANNOVAR_FILE.vcf -s YOUR_SNPEFF_FILE.vcf -c YOUR_CLINVAR_FILE.vcf

• 22annovar.vcf, 22snpeff.vcf and 22clinvar.vcf contain the example data
• ANNOVAR runs a multianalysis but for this project only the MutationTaster predictions are parsed out.
• SnpEff makes predictions for each transcript the variant overlaps but for this project only the prediction for the first transcript is parsed out.
  1. View the results:

##Go to http://bfx3.aap.jhu.edu/chall84/final/fdisplay.html

Search by gene is an exact match. Use the autocomplete for best results.

Search by rs (reference snp from dbSNP) is an exact match. There is no autocomplete.

SnpEff prediction and ANNOVAR prediction are an exact match. Use the list for best results.

Search by diagnosis and clinical significance are not an exact match. Only variants from YOUR_INPUT.vcf will be shown in the results so diagnoses that do not overlap the input variants will have no results.

#Location column: Location is in the format chromosome number > variant start location : reference allele/alternate allele

#Gene column: Pulled from the SnpEff file. Intergenic variants sometimes have more than one gene listed

#Genotype column: HM = homozygous, HT = heterozygous, CHT = compound heterozygous. homozygous and compound heterozygous variants are shaded

#Clinical Diagnosis column: Pulled from the ClinVar file. Mutiple diagnoses are separated by “|”

#RS column: Pulled fom the ANNOVAR file. As current as the ANNOVAR avsnp147 database (or the database you used in the ANNOVAR file)

#Clinical Significance column: Pulled from the ClinVar file. Is specific to the variant allele, not just the location of the variant

#ClinVar variant type column: Refers to the type of mutation rather than its location as the other variant types do

#SnpEff prediction column: More information on interpreting SnpEff predictions is available here: http://snpeff.sourceforge.net/SnpEff_manual.html#input (see Impact prediction category)

#SnpEff variant type column: SnpEff predictions are made based on variant type

#ANNOVAR prediction column: More information on interpreting MutationTaster predictions (provided by ANNOVAR) is available here: http://www.mutationtaster.org/info/documentation.html (see Output category)

#ANNOVAR variant type column: Pulled from the functional refGene annotation in the ANNOVAR file