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filter variant with BED file

asked 2014-01-07 06:16:27 -0700

Vang Le gravatar image

updated 2014-01-09 09:31:42 -0700

I looked around but could not find the answer. I think this question would benefit others so I ask here. I import VCF files from whole exome and gene panel analysis. I want to "activate" variants that are within coordinates specified in a BED file and see some statistics for features in this BED file (i.e. number of variants per feature, coverage per gene). Currently the closest result I can get is the "Variant Classification Count by Gene" report. But it gives report for all genes in the gene track hence shadows the regions of my interest.

Is there a script or trick to get this done?

Thanks

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answered 2014-01-09 09:31:21 -0700

Hi Vang,

GenomeBrowse is a visualization tool only however this is functionality that is available within our SVS software. Direct filtering from the BED files is not supported but you can create an annotation data source of the regions defined in the BED file and then use our region filter to activate variants in your genotype data.

Once your variant list is down to regions of interest then we have tools available that can provide the statistics you are looking to calculate for each region. I will email you with the specific workflows to get this completed.

Please let us know if you have any further questions.

Thanks, Jami...

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Asked: 2014-01-07 06:16:27 -0700

Seen: 13,090 times

Last updated: Jan 09 '14