=== snpEff ===

==== Download data ====

{{{
java -jar /data/CCRBioinfo/biowulf/local/snpEff_3_0/snpEff.jar download -c /data/CCRBioinfo/biowulf/local/snpEff_3_0/snpEff.config GRCh37.66
}}}

==== Run effect prediction ====

{{{
java -jar /data/CCRBioinfo/biowulf/local/snpEff_3_0/snpEff.jar eff -c /data/CCRBioinfo/biowulf/local/snpEff_3_0/snpEff.config GRCh37.66
}}}

=== snpSift ===

==== Annotate with dbSNP ====

{{{
java -Xmx8g -jar /data/CCRBioinfo/biowulf/local/SnpSift_latest.jar annotate  data/CCRBioinfo/public/GATK/bundle/1.5/hg19/dbsnp_135.hg19.excluding_sites_after_129.vcf tmp2.vcf > tmp2.dbsnp.vcf
}}}


==== annotate with dbNSFP =====


{{{
# Donload and uncompress database (you need to do this only once):
# WARNING: The database is 3Gb when compressed and 30Gb uncompressed.
wget http://sourceforge.net/projects/snpeff/files/databases/dbNSFP2.0b3.txt.gz
gunzip dbNSFP2.0b3.txt.gz
}}}

# Annotate using dbNSFP

{{{
java -jar SnpSift.jar dbnsfp /data/CCRBioinfo/public/snpEff/data/dbNSFP2.0b3.txt myFile.vcf > myFile.annotated.vcf
}}}


==== FILTERING ====

{{{
java -Xmx8g -jar /data/CCRBioinfo/biowulf/local/SnpSift_latest.jar filter '(na ID) & (ID =~ 'COSM') & !( ID =~ 'rs')' -f 
}}}