ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome {hg18,hg19,hg38} as well as mouse, worm, fly, yeast and many others).

References:

• ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data, Nucleic Acids Research, 38:e164, 2010).

• ANNOVAR Home
• Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data Nucleic Acids Research, 38:e164, 2010

• Module Name: annovar (see the modules page for more information)
• Multithreaded (table_annovar.pl can utilize multiple threads)
• Environment variables set
  • ANNOVAR_HOME
  • ANNOVAR_DATA
• Example files in $ANNOVAR_HOME/example
• Reference data in /fdb/annovar/current/

ANNOVAR takes text-based input files, where each line corresponds to one variant. On each line, the first five space- or tab- delimited columns represent chromosome, start position, end position, the reference nucleotides and the observed nucleotides. Here is the example file $ANNOVAR_HOME/example/ex1.avinput

1	948921	948921	T	C	comments: rs15842, a SNP in 5' UTR of ISG15
1	1404001	1404001	G	T	comments: rs149123833, a SNP in 3' UTR of ATAD3C
1	5935162	5935162	A	T	comments: rs1287637, a splice site variant in NPHP4
1	162736463	162736463	C	T	comments: rs1000050, a SNP in Illumina SNP arrays
1	84875173	84875173	C	T	comments: rs6576700 or SNP_A-1780419, a SNP in Affymetrix SNP arrays
1	13211293	13211294	TC	-	comments: rs59770105, a 2-bp deletion
1	11403596	11403596	-	AT	comments: rs35561142, a 2-bp insertion
1	105492231	105492231	A	ATAAA	comments: rs10552169, a block substitution
1	67705958	67705958	G	A	comments: rs11209026 (R381Q), a SNP in IL23R associated with Crohn's disease
2	234183368	234183368	A	G	comments: rs2241880 (T300A), a SNP in the ATG16L1 associated with Crohn's disease
16	50745926	50745926	C	T	comments: rs2066844 (R702W), a non-synonymous SNP in NOD2
16	50756540	50756540	G	C	comments: rs2066845 (G908R), a non-synonymous SNP in NOD2
16	50763778	50763778	-	C	comments: rs2066847 (c.3016_3017insC), a frameshift SNP in NOD2
13	20763686	20763686	G	-	comments: rs1801002 (del35G), a frameshift mutation in GJB2, associated with hearing loss
13	20797176	21105944	0	-	comments: a 342kb deletion encompassing GJB6, associated with hearing loss

Reference files are pre-installed in $ANNOVAR_DATA/{build}, where {build} can be either hg18, hg19 or hg38. If other builds are needed, contact staff@hpc.nih.gov. To list all builds currently available, type

ls $ANNOVAR_DATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive -t 4 --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load annovar

[user@cn3144 ~]$ cp $ANNOVAR_HOME/example/ex1.avinput .

[user@cn3144 ~]$ annotate_variation.pl --geneanno --dbtype refGene --buildver hg38 ex1.avinput $ANNOVAR_DATA/hg38

[user@cn3144 ~]$ table_annovar.pl ex1.avinput $ANNOVAR_DATA/hg38 \
  --tempdir /lscratch/$SLURM_JOB_ID \
  --thread $SLURM_CPUS_ON_NODE \
  --buildver hg38 \
  --outfile ex1.out \
  --remove \
  --protocol gene,clinvar_20220320,cosmic70,ljb26_all,avsnp150,cadd_1.5 \
  --operation g,f,f,f,f,f \
  --nastring ''
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. annovar.sh). For example:

#!/bin/bash
set -e
module load annovar
annotate_variation.pl --geneanno --dbtype gene --buildver hg38 ex1.avinput $ANNOVAR_DATA/hg38

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] annovar.sh

Create a swarmfile (e.g. annovar.swarm). For example:

convert2annovar.pl -format vcf4 file1.vcf > file1.inp; annotate_variation.pl --geneanno --dbtype gene --buildver hg38 file1.inp $ANNOVAR_DATA/hg38
convert2annovar.pl -format vcf4 file2.vcf > file2.inp; annotate_variation.pl --geneanno --dbtype gene --buildver hg38 file2.inp $ANNOVAR_DATA/hg38
convert2annovar.pl -format vcf4 file3.vcf > file3.inp; annotate_variation.pl --geneanno --dbtype gene --buildver hg38 file3.inp $ANNOVAR_DATA/hg38
convert2annovar.pl -format vcf4 file4.vcf > file4.inp; annotate_variation.pl --geneanno --dbtype gene --buildver hg38 file4.inp $ANNOVAR_DATA/hg38

Submit this job using the swarm command.

swarm -f annovar.swarm [-g #] [-t #] --module annovar