About MS loci BED file used in MANTIS
Clouate opened this issue · 1 comments
Hi,
I’m not familiar with MANTIS.When running MANTIS on WGS data,I don’t know how to generate the proper MS loci BED file.Because I use Repeatfinder to generate the bed file including MS loci through entire genome. As the answer in:
#40 (comment)
I shouldn’t use the MS loci BED file through entire genome.But I don’t have capture regions(my data is WGS data) or interested region.How can I filter my MS loci bed?
I want to know if these two approaches work:
1)select protein coding gene region
2)select MS loci that MANTIS paper uses for TCGA data
Are there any approaches for WGS data?
Thanks!
Hello Leon352,
If you are interested in MSI vs. MSS calls, I would recommend just using the loci from the MANTIS paper (attached, coordinates in hg19), and in addition using the suggested quality thresholds for whole exome data (https://github.com/OSU-SRLab/MANTIS#whole-exome-usage). Please let us know if you have any additional questions or encounter difficulties.