Instructions for Input CSV and Pipeline Flags

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
```
When running the pipeline, specify the flag:
```
--coverage_stats true
```
If you only need regulatory regions of the genome, also specify the flag:
```
--intersect true
```

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