snpswift

snpswift annotates variants in a VCF file with VCF or GTF databases.

            

            
$ pbrun snpswift \
    --input-vcf input_to_be_annotated.vcf \
    --anno-vcf prefix1:source_of_annotations_1.vcf.gz \
    --anno-vcf prefix2:source_of_annotations_2.vcf.gz \
    --output-vcf the_annotated_version.vcf
        

If the --ensembl option (see below) is used, snpswift requires that the chromosome names be prefixed with 'chr'. If the chromosome names do not already have a 'chr' prefix it can be added with the following command:

            

            
$ awk '{if($0 !~ /^#/) print "chr"$0; else print $0}' < Homo_sapiens.GRCh38.104.gtf > Homo_sapiens.GRCh38.104.withchr.gtf
        

In cases where there are multiple matches for a query variant in a single annotation database, snpswift will annotate with details from the first match found. For example, given this query variant:

and these matches in a single database:

Snpswift annotation uses the information from the first match to produce this:

If the input VCF file contains multi-allelic variants we suggest splitting the multi-allelics with bcftools before using snpswift for optimal annotation coverage:

            

            
$ bcftools norm --multiallelics- multiallelic_variants.vcf -o input_to_snpswift.vcf
        

Annotate a VCF file using VCF and GTF databases.

Input/Output file options

Options specific to this tool

Common options: