Run ABSOLUTE with allelic copy ratio on hg38

[YingYa]

How could I run this version of ABSOLUTE with allelic copy ratio on hg38?
What is the input format for maf and seg files?

Thanks

[julianhess]

Hi,

Have you run ABSOLUTE before (on hg19)? If so, any hg38 seg files and MAFs generated by that pipeline will be compatible with the ABSOLUTE code in this repo; you just need to remove "chr" in front of contig names (e.g. "chr1" -> "1").

—Julian

[YingYa]

Hi，

Two versions (absolute_wolf:v6 and absolute_wolf:no_indel_filter_v6) are used in tasks.py, I want to run ABSOLUTE on a local cluster, should I pull both versions or only the latest one (absolute_wolf:no_indel_filter_v6)?

Thanks

[julianhess]

absolute_wolf:v6 will probably work for your needs. By default, ABSOLUTE does not consider indels in noncoding regions, since they overwhelmingly occur at microsatellites (which are especially artifact-prone), and thus have distorted alt/ref counts, which makes it difficult to assign them multiplicities/CCFs.

If, however, you have very well-filtered whole genome calls and are interested in computing multiplicities/CCFs for noncoding indels, then use the no_indel_filter version.