How to get HGVS notation of protein form genome snp vcf
Hi everyone
I want to do variation annotation with PROVEAN (http://provean.jcvi.org/seq_submit.php) on non-module organisms, I have got protein sequence of my study species from MAKER, also got snp VCF file from GATK, but I can not get HGVS notation of protein sequence of my study organisms. Could you please tell me which tools could do this stuff? Thank you very much.
• 2,102 views
•
link
updated
by
Biostar
•
written
by
yixinrufeng •
•
written
by
yixinrufeng •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
MAKER: how to use RNAseq data to assist annotation?
written by bbscience •
-
error: BLAST database name is missing. Please edit provean.sh file to add the name.
written by elham •
-
dbSNP with RefSeq chromosome notation
written by Tom •
-
filter VCF by HGVS - indel normalisation
written by michal.inbar •
-
Maker Genome Annotation - protein isoforms
written by luca •
-
Variant caller comparison for non-human data (highly varied populations)
written by hermathena •
-
extract SNPs corresponding position on BLAST subject sequence
written by pbigbig
-
How identify zero fold degenerate sites
written by yixinrufeng •
-
How identify zero fold degradation sites
written by yixinrufeng •
-
Parsing error with Provean : Someone else ?
written by jsgounot
Hi, What do you mean ? Do you want HGVS annotation of protein but for an other organism than Human ?
Yes， you are right, not for Human.