Instructions for Input CSV and Pipeline Flags

1. Add the special fields family_member and family to the input CSV file.

   1.1) Add them to the file header (example header line):

   patient,sample,lane,fastq_1,fastq_2,family_member,family
   

   1.2) For each data row, append who the person is in the trio (mother, father, child) and the trio number (if there is only one trio, set 1 for all; if there are multiple trios, use subsequent numbers accordingly). Example rows:

   ID1,S1,L002,/out.fq.gz,/out2.fq.gz,child,1
   ID2,S2,L002,/out.fq.gz,/out2.fq.gz,father,1
   ID3,S3,L002,/out.fq.gz,/out2.fq.gz,mother,1
   

2. When running the pipeline, specify the flag:

   --coverage_stats true

3. If you only need regulatory regions of the genome, also specify the flag:

   --intersect true