Hi,

I have a list of variants called from a individual genome and I'm trying to filter out the important predispositions from it. My approach was to download the `variant_summary.txt.gz` file from ClinVar website, in which most of the variants related to human health are being recorded, so that I can intersect my variants with it.

I loaded the `variant_summary.txt` into R and it says the Dataset has 154358 rows and 25 columns. But when I check with `wc-l` linux the number of records is 198661. I double checked the no of rows by visualizing the data in excel. It had 198,661. My questions are,

1. Why R does not load all the records of my file?
2. Given the fact that I'm still novice to bioinformatics do you think that my approach is feasible in finding predispositions if I fix the R issue?

Thanks you very much.
You can read in the file like so:

```
var.anno = read.delim("Downloads/variant_summary.txt", header=T)
dim(var.anno)
[1] 198660     25
```

That gave me the correct dimensions, first row contains the header.

Regarding your second question, I think it is reasonable to try to annotate detected variants and their association with phenotypes from available databases. Depending on what you are after, you might also want to consult other variant databases, e.g. dbSNP. dbSNP also links to ClinVar if there is [an entry there][1] and to OMIM.

There are also R packages for this purpose, some here:

 - http://cran.r-project.org/web/packages/NCBI2R/index.html
 - SNP-related packages in bioconductor http://www.bioconductor.org/packages/release/BiocViews.html#___SNP

 [1]: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=4988235