Use additional resources - zwdzwd/transvar GitHub Wiki

TransVar uses optional additional resources for annotation.

dbSNP

For example, one could annotate SNP with dbSNP id by downloading the dbSNP files. This can be done by

transvar config --download_dbsnp

TransVar automatically download dbSNP file which correspoding to the current default reference version (as set in transvar.cfg). This also sets the entry in transvar.cfg. With dbSNP file downloaded, TransVar automatically looks for dbSNP id when performing annotation.

$ transvar panno -i 'A1CF:p.A309A' --ccds

A1CF:p.A309A	CCDS7243 (protein_coding)	A1CF	-
   chr10:g.52576004T>G/c.927A>C/p.A309A	inside_[cds_in_exon_7]
   CSQN=Synonymous;reference_codon=GCA;candidate_codons=GCC,GCG,GCT;candidate_sn
   v_variants=chr10:g.52576004T>C,chr10:g.52576004T>A;dbsnp=rs201831949(chr10:52
   576004T>G);source=CCDS

Note that in order to use dbSNP, one must download the dbSNP database through transvar config --download_dbsnp, or by configure the dbsnp slot in the configure file via transvar config -k dbsnp -v [path to dbSNP VCF]. Manually set path for dbSNP file must have the file tabix indexed.