Entering edit mode

3.0 years ago

merobin8
•
0

I need to calculate the position (e.g. c.4879+41) of "Mutation Call:Relative To CDS (e.g c.4879+41delG)" base on file HG19 RefGene with info like [txName] ,[chrom] ,[strand] ,[txStart] ,[txEnd] ,[cdsStart] ,[cdsEnd] ,[exonCount] ,[exonStarts] ,[exonEnds] ,[score] ,[geneName] ,[cdsStartStat] ,[cdsEndStat] ,[exonFrames].

However , some of my result can match , some are not . Is there anyone know the algorithm of this calculations ?

**Below are some examples :**

```
**NextGene Output My Result**
c.1-33T>C c.1-33
c.294A>G c.294
c.728-47A>G c.728-47
c.728-45C>G c.728-45
c.728-39C>A c.728-39
c.728-39C>G c.728-39
c.1178-6T>C c.1178-6
c.1384+28G>A c.1384+28
c.1385-15_1385-14delCT c.1385-15
c.1385-15_1385-14delCT c.1385-14
c.2537-26A>G c.2537-26
c.3011T>C c.3011
c.3066A>G c.3066
c.3517-12T>C c.3517-12
c.3558T>C c.3558
c.4161T>C c.4161
c.4299-48T>G c.4299-48
c.4745-17C>T c.4745-17
c.4879+41delG c.4879+27
c.4879+32G>A c.4879+32
c.4879+33G>A c.4879+33
c.4879+43T>C c.4879+43
c.5651+5C>T c.5651+5
c.6057C>T c.6057
c.534G>A c.534
c.57+41C>A c.58+41
```

What is the gene name or transcript name?

Could you add some more details about your input and desired output?

For me it looks like you have a list of variants in hgvs notation and you like to get rid of the base changes informations leaving behind only the

`c.`

position?Why this entry appears two times with different result?

fin swimmer

Thanks for your reply . What I want to do is to generate the same result as the nextgene output (column left) by only process the refGene database with chr + chrPos+ transcript name+ gene name. However, what i can do for now is to calculate the c. position first 。 What I post is just a few example for reference only . For now I don't have a full pictures of how the c. position is calculated . It seems that it have many condition to consider . Now my algorithm can fit for some condition ,but others are not . Since I am new to this area , I hope if some one can provide the full pictures of how the do this . Below are some of the records are not matched for reference only .

Hello merobin,

now I've got it I think :)

I cannot provide an algorithm, but i checked your results using mutalyzer. The result is that (most) of your c. position are correct and not the one from nextgene. For variants with

`+`

you have a off-by-one problem. So e.g.`c.200+30`

should be`c.199+30`

.fin swimmer