How to determine some parameters in YAML files

[evayfang2019]

Hi Dr. Chen,
I'm curious about some of the settings in the ./data/38/config.yaml. Could you please tell me some of the details?
Thank you!

Taking Amy1A as an example

AMY1A:
  genes: AMY1A,AMY1B,AMY1C
  realign_region: chr1:103650157-103669000
  extract_regions: chr1:103650158-103668000 chr1:103684093-103701812 chr1:103744296-103762027
  left_boundary: 103650159
  right_boundary: 103667870
  clip_3p_positions: [103667876]
  noisy_region: [[103667000, 103667870]]
  add_sites: ["103667950_T_A"]
  use_supplementary: True

genes: name of target gene (AMY1A) and its pseudogene (AMY1B,AMY1C)
realign_region: may be related to the region of AMY1A, and how to determine this specific location?
extract_regions: may be related to the region of AMY1A and its pseudogene (AMY1B,AMY1C), and how to determine?
as well as left_boundary, right_boundary, clip_3p_positions, noisy_region, add_sites, use_supplementary and other parameters?

[xiao-chen-xc]

What Paraphase really needs are realign_region and extract_regions. extract_regions specifies where you want to extract relevant reads from the input bam, i.e. all the homologous regions (e.g. SMN1 and SMN2). realign_region is where you want all the extracted reads to be realigned to, i.e. one region selected to represent the group (e.g. SMN1). All the other parameters are optional and used to optimize the phasing result. If you have regions of interest to add to Paraphase, I can help with selecting and optimizing the parameters. Feel free to discuss them here or email me (xchen@pacb.com).