Documentation

[ofonov]

Hi, It would be great to have more detailed documentation, in particular:

• Format of bed file with various CNVs, how one should format it for hom/het duplications, deletions, etc.
• How one can model specific VAFs for inserted mutations?
• Does one need to supply only bam files split by @SQ, or do these files need to be sorted by name, or does the tool require both type of files (chr#.bam and chr#.byname.bam)? Since software is fairly resource demanding, it's quite time consuming figuring out these details by trial and error. Thanks!