RefSeq hg19

[sarmadym]

--refseq switch for hg19 annotation uses annotation release 105 which is a bit old. I understand that NCBI switched to GRCh38 reference for their provided refseq gff files for subsequent releases. Is there a way to have transvar work with UCSC RefSeq downloaded files?

[Wanding Zhou - Bioinformatics]

Sorry just saw this. Reposting my answers here in case others are curious:

1. in UCSC table browser, choose hg19, gene annotation, refseq, "all fields from selected table" as output, save as ucsc.refgene.hg19.txt.gz

2. transvar index --ucsc ~/Downloads/ucsc.refgene.hg19.txt.gz, this will create a bunch of transvardb*

Now we can use the latest RefSeq with hg19.
3) transvar ganno -i "chr4:g.144918713T>C" --ucsc ~/Downloads/ucsc.refgene.hg19.txt.gz.transvardb
input transcript gene strand coordinates(gDNA/cDNA/protein) region info
chr4:g.144918713T>C NM_001304382 (protein_coding) GYPB - chr4:g.144918713T>C/c.172A>G/p.S58G inside_[cds_in_exon_5] CSQN=Missense;codon_pos=144918711-144918712-144918713;ref_codon_seq=AGT;source=UCSCRefGene
chr4:g.144918713T>C NM_002100 (protein_coding) GYPB - chr4:g.144918713T>C/c.250A>G/p.S84G inside_[cds_in_exon_4] CSQN=Missense;codon_pos=144918711-144918712-144918713;ref_codon_seq=AGT;source=UCSCRefGene