Biowulf at the NIH
RSS Feed
SIFT on Biowulf

Description

SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.

How to Use

SIFT uses environment modules. Type

module load SIFT

SIFT scores for mutations can be run using a FASTA file aligned to a reference database.

seqs_chosen_via_median_info.csh $SIFTHOME/test/lacI.fasta /fdb/blastdb/nr 2.75
cp $SIFT_SCRATCHDIR/lacI.alignedfasta .

SIFT can also generate scores for variants. The databases for SIFT are located in $SIFTDB.

SIFT_exome_nssnvs.pl -i $SIFTHOME/test/snvs_build37.input \
-d $SIFTDB/Human_db_37 -o $SIFT_SCRATCHDIR -z output.tsv

Here is an example SIFT script to run on the cluster:

# this file is sift_script.sh
clearscratch
module load SIFT
SIFT_exome_nssnvs.pl -i $SIFTHOME/test/snvs_build37.input \
-d $SIFTDB/Human_db_37 -o $SIFT_SCRATCHDIR -z output.tsv

Then, submit to a g24 node, since these nodes have at least 120GB of disk space on /scratch:

qsub -l nodes=1:c16:g24 sift_script.sh

Documentation