BedToIntervalList (Picard) and IntervalListTools (Picard)

Question

[Beyza]

Hi,

I am developing a variant calling pipeline in Snakemake for my master's thesis and I would love to hear about your ideas on one thing.

What do BedToIntervalList and IntervalListTools do exactly, and are they essential? Depending on my research and examination of current pipelines, it is not an essential step in the RNA-Seq variant calling pipeline. I saw it in nfcore/rnavar (https://github.com/nf-core/rnavar/tree/master) and trying to understand their biological importance. Happy to hear your thoughts about it!

Thanks

Answer 1

[Pierre Lindenbaum]

The *interval_list is a file format that defines interval just like a BED file (although is 1-based while bed is a 0-based half-open interval). IMHO, what's interesting in the interval_list format is that it includes a SAM header where you can put a bunch of meta data (sample name, etc...). And, most important, there is a dictionary (lines starting with "##contig=" ) which allow you to identify the REFerence genome without ambiguity. There is no need to worry about the origin of the BED file (is it hg19 , is it hg38 ?) and to join/merge data (hg19 vs hg38).