isanwong / snpeff-1

snpEff with HGVS annotations for nucleotide changes ***NOT THE OFFICIAL snpEff REPOSITORY***

snpEff with HGVS

This codebase is branched off of official SnpEff version 3.1h (http://snpeff.sourceforge.net/).

Setup

The snpEff make script assumes a specific Eclipsey directory structure. Let's not muck with that.

mkdir ~/workspace ~/snpEff
cd ~/workspace
git clone [email protected]:CBMi-BiG/snpEff.git SnpEff
cd SnpEff

Maven/Ant/Ivy have a hard time getting Picard and Samtools jars, but they are in the Picard distribution. Alter the pom.xml versions as necessary.

wget http://downloads.sourceforge.net/project/picard/picard-tools/1.84/picard-tools-1.84.zip
unzip picard-tools-1.84.zip
mvn install:install-file -DgroupId=net.sf.samtools -DartifactId=Sam -Dversion=1.84 \
-Dpackaging=jar -Dfile=$PWD/picard-tools-1.84/sam-1.84.jar
mvn install:install-file -DgroupId=net.sf.picard -DartifactId=Picard -Dversion=1.84 \
-Dpackaging=jar -Dfile=$PWD/picard-tools-1.84/picard-1.84.jar

CHANGELOG

3.1h2 Introduces proper HGVS for insertions and deletions, including those which require "walking and rolling" to identify the correct indel frame.

To build snpEff-3.1-jar-with-dependencies.jar in the ~/workspace/SnpEff/target directory:

./scripts/make.sh

This is copied to ~/workplace/SnpEff/snpEff.jar per the config file

To get GRCh37 annotations:

mkdir -p data/GRCh37.64
java -jar snpEff.jar download GRCh37.64

To test (assuming you have downloaded all the test cases):

java -cp snpEff.jar \
ca.mcgill.mcb.pcingola.snpEffect.testCases.TestSuiteAll

java -Xmx4g -jar snpEff.jar hg19 -i vcf -o vcf tests/hgvs_test_in.vcf

Output

This fork of SnpEff introduces the following annotations to VCF files

• Segment (previously Exon) - a verbose description of exons (e.g. NM_152486.2.ex.3) or introns (NR_024540.1_intron_7) for all applicable transcript hits
• HGVS_DNA_nomenclature HGVS coding DNA nomenclature for exonic SNPs e.g. NM_001005484.1:c.655C>T. See http://www.hgvs.org/mutnomen/recs-DNA.html for more info.

VCF output example

##SnpEffVersion="SnpEff_cbmi 3.1h (build 2013-06-12), by Pablo Cingolani"
##SnpEffCmd="SnpEff  hg19 -i vcf -o vcf tests/hgvs_test_in.vcf "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Rank | Segment | HGVS_DNA_nomenclature | HGVS_protein_nomenclature [ | ERRORS | WARNINGS ])' ">
#CHROME POS     ID      REF     ALT     QUAL    FILTER  INFO
1	16856	.	A	G	100.0	PASS	DP=100;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1||NON_CODING|NR_046018.2||||),INTRON(MODIFIER|||||WASH7P||NON_CODING|NR_024540.1|7|NR_024540.1_intron_7||),SPLICE_SITE_DONOR(HIGH|||||WASH7P||NON_CODING|NR_024540.1|7|NR_024540.1.ex.5||)
1	69745	.	C	T	100.0	PASS	DP=100;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q219*|305|OR4F5||CODING|NM_001005484.1|1|NM_001005484.1.ex.1|NM_001005484.1:c.655C>T|p.Q219*)
1	865697	.	A	G	100.0	PASS	DP=100;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I79V|681|SAMD11||CODING|NM_152486.2|3|NM_152486.2.ex.3|NM_152486.2:c.235A>G|p.I79V)
1	1114650	.	C	T	100.0	PASS	DP=100;EFF=STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R19*|673|TTLL10||CODING|NM_001130045.1|4|NM_001130045.1.ex.4|NM_001130045.1:c.55C>T|p.R19*),UPSTREAM(MODIFIER||||404|TTLL10||CODING|NM_153254.2||||)

txt output example

# SnpEff version SnpEff_cbmi 3.1h (build 2013-06-12), by Pablo Cingolani
# Command line: SnpEff  hg19 -i vcf -o txt tests/hgvs_test_in.vcf 
# Chromo	Position	Reference	Change	Change_type	Homozygous	Quality	Coverage	Warnings	Gene_ID	Gene_name	Bio_type	Trancript_ID	HGVS_DNA	HGVS_AA	Exon_ID	Exon_Rank	Effect	old_AA/new_AA	Old_codon/New_codon	Codon_Num(CDS)	Codon_Degeneracy	CDS_size	Codons_around	AAs_around	Custom_interval_ID
1	16856	A	G	SNP	Hom	100	100		WASH7P	WASH7P		NR_024540.1					INTRON								
1	16856	A	G	SNP	Hom	100	100		DDX11L1	DDX11L1		NR_046018.2					DOWNSTREAM: 2447 bases								
1	16856	A	G	SNP	Hom	100	100		WASH7P	WASH7P		NR_024540.1			NR_024540.1.ex.5	7	SPLICE_SITE_DONOR								
1	69745	C	T	SNP	Hom	100	100		OR4F5	OR4F5		NM_001005484.1	NM_001005484.1:c.655C>T	p.Q219*	NM_001005484.1.ex.1	1	STOP_GAINED	Q/*	Cag/Tag	219	1	918			
1	865697	A	G	SNP	Hom	100	100		SAMD11	SAMD11		NM_152486.2	NM_152486.2:c.235A>G	p.I79V	NM_152486.2.ex.3	3	NON_SYNONYMOUS_CODING	I/V	Atc/Gtc	79	1	2046			
1	1114650	C	T	SNP	Hom	100	100		TTLL10	TTLL10		NM_001130045.1	NM_001130045.1:c.55C>T	p.R19*	NM_001130045.1.ex.4	4	STOP_GAINED	R/*	Cga/Tga	19	2	2022			
1	1114650	C	T	SNP	Hom	100	100		TTLL10	TTLL10		NM_153254.2					UPSTREAM: 427 bases					1215