Snow

we should keep the unresolved SVs from manta tloc resolve, and cluster them in the same way as manta/wham SVs

updated the AF annotation scripts to : 1. revise "pop_AF" to "AF_pop" 2. added "CN_STATUS"

Shall we consider adding mobile element insertions as independent variant type in MainVcfQc?

1. copy number of each sample should be counted for mCNVs, and non-ref samples in mCNV should be included in the output bed file when using `svtk vcf2bed` (currently no...

I saw a subset of MEI have the alt column revised from (ALU as an example but this happens for all MEI types) to . These insertions have the expected...

suggestions: 1. add STRANDS information to the manta_tloc file? we can either add a patch to add it after svtk resolve , or can update svtk to add the information...