Question: Creating alternate Bed file by incorporating INDELs locations
0
gravatar for ersgupta
3.8 years ago by
ersgupta0
Potsdam, Germany
ersgupta0 wrote:

I have a exome bed file (coordinates wrt to ref genome) and a bed file with coordinates of INDELs (incorporated in ref genome). Now I want to generate a modified exome bed file which can shift the coordinates wrt to INDEL event.

For. eg. 

exome bed file:
chr1 10 100
chr1 200 400

indels file:
chr1 120 150 deletion

output exome bed file:
chr1 10 100
chr1 170 370
sequencing sequence • 1.1k views
ADD COMMENTlink written 3.8 years ago by ersgupta0

You might have to write a little program to do this for you. Thankfully with just BED files this is rather more doable.

ADD REPLYlink written 3.8 years ago by Devon Ryan91k

Yeah, was planning to do that. But just thought to ask if anyone already has a script for this. It would be great if there was something like FastaAlternateReferenceMaker for bed files, I guess will have to write on my own.

ADD REPLYlink written 3.8 years ago by ersgupta0
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