I have some BAMs from whole exome sequencing.
I want to run GATK haplotype caller, which requires one bed file as input
SureSelect kit for the BAMs comes with 4 different .bed files:
Googling shows this question has been asked multiple times: What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
I still don't know, but my gut instinct is to use the
*_Padded.bed file because according to agilent it shows:
"the genomic regions that you can expect to sequence when using the design for target enrichment. To determine these regions, the program extends the regions in the Covered BED file by 100 bp on each side."
Has anyone done this before and know the way?