Output format for trio calling
The output format is a single row for each putative de novo mutation (DNM), with the following fields
1. Event type (POINT MUTATION or INDEL).
2. CHILD_ID - sample ID of trio-offspring with the DNM.
3. chr - chromosome.
4. pos - physical Position.
5. ref - base present in reference sequence at this position (from BCF).
6. alt - comma separated list of alternate non-reference alleles called on at-least one sample (from BCF).
7. maxlike_null - likelihood of the most likely mendelian-compatible genotype configuration.
8. pp_null - posterior probability of the most likely mendelian-compatible genotype configuration.
9. tgt_null(child/mom/dad) - genotypes of the most likely mendelian-compatible configuration.
10. snpcode - code that indicates whether the configuration shown in field 6 is monomorphic (1) or contains variation (2)(internal filters, can be ignored).
11. code - This field seems to be redundant to field 7, except the codes are (6) and (9).(internal filters, can be ignored).
12. maxlike_dnm - likelihood of the most likely DENOVO genotype configuration.
13. pp_dnm - posterior probability of the most likely DENOVO genotype configuration.
14. tgt_dnm(child/mom/dad) - genotypes of the most likely mendelian-compatible configuration.
15. lookup - Code that indicates if the most likely DNM is a transition (4) or transversion (5) (for development use only).
16. flag - Flag that indicates whether the data for the site passed internal QC thresholds (for development use only).
17-19. Read depth of child, parent 1 and parent 2.
20-22. Root mean square of the mapping qualities of all reads mapping to the site for child, parent 1 and parent 2. Currently these values are the same for all samples when using BCF as the input format.