Pathogenic Variants in a Genomic interval

Question

[tylertibetli]

Hello Guys,

I would like to ask that if it is possible to find all the Clinvar pathogenic mutations in a given genomic interval. After an RNA-seq analysis, I got more than 100 genomic intervals as a BED file and I didn't find an easy way to find all the pathogenic mutations in the genomic intervals. Any help would be appreciated.

Thank you,

[ATpoint]

You can download the VCF from ClinVar and then use tabix to retrieve all variants overlapping with your intervals. From there on, filter for variant classification being pathogenic.

[tylertibetli]

Thank you for assistance, I ve downloaded Clinvar records as VCF, but tabix is not working properly for the overlapping. I' ve sorted VCF and Bed files but appearing some errors such as "[ti_index_core ] the file out of order at line 5" . Should I remove the header lines of VCF?

Answer 1

[Emily]

You could use BioMart. Use the short variation database, filter by your genomic region and clinical significance.

[tylertibetli]

Dear Emily, thank you for the help, I tried the website and want to ask that is possible to upload BED file for the region, it didn' work and I 've changed the format of BED file as 1:123425:112356:1 , but still didn't return back any data I didn't understand the problem :(

[Emily]

It's because there aren't any.