Entering edit mode
5.5 years ago
merobin8
•
0
I have got Clinvar,vcf database and uploaded to SQL Sever . This database have field CHROM , POS, REF , ALT .
Now I want to use CHROM , POS, REF , ALT AS key to match the record to get CLNSIG .
For 'del' and 'ins' case ,how to get the correct REF , ALT from MutationCallRelativeToCDS to match the database ? Is there any rules ?
Below are some examples :
c.3285-15delA
c.3659+19delA
c.3811+60_3811+61insT
c.3811+60delT
c.4229-33delT
c.357-36_357-35insC
c.866+33_866+34insT
c.866+47delC
c.2017-27_2017-26insC
c.358+44_358+46delTCT
c.358+44_358+46delTCT
c.358+44_358+46delTCT
c.866+33_866+34insT
c.866+47delC
c.2017-29_2017-28insC
c.823+33delG
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.409-50delG
c.866+48_866+49insAGGCAACC
c.1114+36_1114+37insA
Below are how the datebase looks like :
POS ID REF ALT QUAL FILTER
949422 475283 G A . .
949502 542074 C T . .
949523 183381 C T . .
949559 542075 C T . .
949597 475278 C T . .
949608 402986 G A . .
949696 161455 C CG . .
949739 161454 G T . .
949781 542076 G A . .
Either you back calculate and match or calculate csyntax and match
Hello,
I don't know the program MutationCallRelativeToCDS. Can you link to it?
I hope you have at least gene names, but better transcript id's, to your
c.
variants. Otherwise there is no chance to convert them to genomic position.The most easiest way to convert hgvs variants to genomic positions is to use VEP. If you use gene names instead of transcript id's be aware that the result might be ambiguous.
fin swimmer