channels_list.md

List of channels:

1. depth of coverage
2. one hot encoding for A
3. one hot encoding for C
4. one hot encoding for T
5. one hot encoding for G
6. one hot encoding for N
7. number of SOFT clipped reads on the LEFT in FWD direction
8. number of SOFT clipped reads on the RIGHT in FWD direction
9. number of SOFT clipped reads on the LEFT in REV direction
10. number of SOFT clipped reads on the RIGHT in REV direction
11. number of reads with an CIGAR "I" in FWD direction
12. number of reads with an CIGAR "I" in REV direction
13. number of reads with a number of mismatches (NM) equal to or greater than 11 and minimum mapping quality of 15
14. number of reads SOFT clipped in both directions
15. number of reads with CIGAR "D" in FWD direction
16. number of reads with CIGAR "D" in REV direction
17. number of split reads with mapping quality lower than 10
18. number of inter-chromosomal split reads
19. number of paired reads where the mate is unmapped
20. number of SPLIT reads with PLUS PLUS orientation
21. number of SPLIT reads with MINUS MINUS orientation
22. number of SPLIT reads with MINUS PLUS orientation
23. number of SPLIT reads with PLUS MINUS orientation
24. number of DISCORDANT reads with PLUS MINUS orientation
25. number of DISCORDANT reads with PLUS PLUS orientation
26. number of DISCORDANT reads with MINUS MINUS orientation
27. number of DISCORDANT reads with MINUS PLUS orientation
28. (orphans) number of SPLIT reads with PLUS PLUS orientation
29. (orphans) number of SPLIT reads with MINUS MINUS orientation
30. (orphans) number of SPLIT reads with MINUS PLUS orientation
31. (orphans) number of SPLIT reads with PLUS MINUS orientation
32. (orphans) number of DISCORDANT reads with PLUS MINUS orientation
33. (orphans) number of DISCORDANT reads with PLUS PLUS orientation
34. (orphans) number of DISCORDANT reads with MINUS MINUS orientation
35. (orphans) number of DISCORDANT reads with MINUS PLUS orientation