If I want to restrict variant calling over my own target BED, which workspace attributes can I use to point to my target BED?
What is the difference between AGILENT_INTERVALS and MUTECT_FC_INTERVALS?
Hi @severinec . The MUTECT_FC_INTERVALS is used in the "force calling" and is for "hot spots" (e.g. p53). The AGILENT_INTERVALS is for targeting the sequenced exome. You could theoretically replace with your own intervals, but the AGILENT_INTERVALS replace might be more optimized.
Is it mandatory to have the *INTERVALS attributes included in a workspace, or can I have a workspace without INTERVALS, i.e., the calling would be unrestricted over the entire BAM?
The WDL has the file as required and for the method configuration to run an interval file must be provided. The file provided in your case is configured to be provided via the workspace (see the summary tab). However, the file may be provided via the data entity model (e.g. via "this.my_reference") or alternatively via a file literal (using double quotes) (e.g. "gs://mybucket/path/to/myfile.interval_list"). Check out https://software.broadinstitute.org/firecloud/documentation/. In particular, this slideset https://drive.google.com/file/d/0B60rEaYX69a9d1p4eE90WW9mTW8/view (near slides 38-52 might be particuarly informative/helpful)
It sounds like you want a WGS analysis...is that right?
What I do when I want to run a WGS analysis is I use a WGS interval list in the config, I use one of these:
The "1_22XYMT" file includes the normal chromosomes 1....22, X, Y, and MT (for a total of 25 reference sequences). The ".wgs_intervals.interval_list" file ("plain") includes all the contigs (e.g. GL) for a total of 85 reference sequences. I usually use the "1_22XYMT" file because analysis requirements deem no interest in variants on the "GL" sequences.
Thank you that's helpful.
What about the TCGA exomes, what INTERVAL file do you use for that?
The TCGA exome file used is gs://firecloud-tcga-open-access/tutorial/reference/whole_exome_agilent_1.1_refseq_plus_3_boosters_plus_10bp_padding_minus_mito.Homo_sapiens_assembly19.targets.interval_list