从 p.HGVS 到基因组变异位置

transcvar web 版

transcvar 本地化

# https://github.com/zwdzwd/transvar
pip search transvar
pip install transvar --user

transvar config --download_ref --refversion hg19
transvar config --download_anno --refversion hg19

head HGVS_cds
# MLH1:c.100G>A
# MLH1:c.790+1G>A
# VHL:c.1_17del17
# VHL:c.136G>T

transvar canno --refversion hg19 --refseq -l HGVS_cds --oneline >HGVS_cds.transvar.txt

head HGVS_cds.transvar.txt
# input	transcript	gene	strand	coordinates(gDNA/cDNA/protein)	region	info
# MLH1:c.100G>A	NM_001167618 (protein_coding)	MLH1	+	chr3:g.37059029G>A/c.100G>A/p.A34T	inside_[cds_in_exon_10]	CSQN=Missense;reference_codon=GCC;alternative_codon=ACC;dbxref=GeneID:4292,HGNC:7127,HPRD:00390,MIM:120436;aliases=NP_001161090;source=RefSeq
# MLH1:c.790+1G>A	NM_001258271 (protein_coding)	MLH1	+	chr3:g.37056036G>A/c.790+1G>A/.	inside_[intron_between_exon_9_and_10]	CSQN=IntronicSNV;dbxref=GeneID:4292,HGNC:7127,HPRD:00390,MIM:120436;aliases=NP_001245200;source=RefSeq
# VHL:c.1_17del17	NM_198156 (protein_coding)	VHL	+	chr3:g.10183532_10183548del17/c.1_17del17/.	inside_[cds_in_exon_1]	CSQN=CdsStartDeletion;left_align_gDNA=g.10183529_10183545del17;unaligned_gDNA=g.10183532_10183548del17;left_align_cDNA=c.1-3_14del17;unalign_cDNA=c.1_17del17;cds_start_at_chr3:10183532_lost;dbxref=GeneID:7428,HGNC:12687,HPRD:01905,MIM:608537;aliases=NP_937799;source=RefSeq

类似的也可以从 c.HGVS、g.HGVS 开始获得完整注释

本地化数据库配置

软件提供数据库路径为：http://transvar.info/transvar_user/annotations/，本地数据库配置详细如下：