Why are BED files necessary for somatic calling?
Apologies if this is an elementary question, but why are BED files necessary (if at all) for somatic mutation callers, other than to simply speed up the calling by restricting calling to certain regions? I see an option to specify calling in certain regions. Does it actually improve the calling sensitivity/specificity at all?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Can germline callers detect somatic variants? (RNAseq, cancer, no matched normal)
written by don •
-
Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data?
written by wangziwei0010 •
-
Mutect2 missing mutations
written by vctrm67 •
-
Extract the overlap of well-covered regions across multiple samples
written by DVA
-
How to do a local denovo assembly including unmapped paired reads for many samples to genotype a la…
written by William
-
Faster way to get coverage per base
written by finswimmer
-
Finding reads having more than one mutation in BAM file
written by marki
-
The problem with sensitivity analysis of somatic variant caller
written by phongphak.06 •
-
How to build a custom reference genome (from a BED file)
written by umn_bist •
-
Doubts in Agilent Sure select DNA design
written by Amk
No, these files are not necessary but typically can be used to specify regions in order to reduce runtime.