I'm using ANNOVAR to annotate variants from somatic sequencing data. I first annotate my VCF files with snpEff, which accurately picks up on mutliple variants at a single locus. I then annotate with ANNOVAR, which seemingly is unable to handle the comma separating variants, and only annotates the first in a comma delimited list of variants. Here is an example: I have in order, chromosome, position, REF, ALT, snpEff_Allele, and REVEL score. The REVEL score should be 0.545 for row 1, and 0.698 for row 2 and 3.
chr4 118705648 G A,C A 0.545 chr4 118705648 G A,C C 0.545 chr4 118705648 G C C 0.698
According to documentation, ANNOVAR should be able to handle this kind of format but seemingly not? This is the code I used to run ANNOVAR.
module load annovar/2018-04-16 perl $ANNOVAR_HOME/table_annovar.pl /path/to/file.vcf $ANNOVAR_DATA/hg38 \ -buildver hg38 -out /path/to/output.vcf \ -protocol exac03nontcga,gnomad_genome,gnomad_exome,esp6500siv2_all,dbnsfp33a,revel,clinvar_20170130,intervar_20180118 -operation f,f,f,f,f,f,f,f \ -nastring . -vcfinput