Are Ns counted into DEPTH?

[Y-Pei]

Many thanks for the extremely fast tool!

In the doc it says:

DEPTH          The total depth at the position SUM(A, C, T, G, DEL)

While from our test data, it seems that Ns are also counted into DEPTH:

REF  	 POS      	 REF_BASE	 DEPTH 	 A     	 C     	 G     	 T     	 N    	 INS	 DEL	 REF_SKIP	 FAIL	 NEAR_MAX_DEPTH
chr1 	   2228805	 G       	  37139	     51	      1	  23423	      9	 13655	   0	   0	        0	  118	 false
chr1 	   2228806	 C       	  37206	      1	  32028	      0	      6	  5171	   0	   0	        0	  120	 false
chr1 	   2228807	 A       	  37344	  30049	     17	      3	      8	  7267	   0	   0	        0	  119	 false
chr1 	   2228808	 C       	  37977	      4	  32878	      1	      4	  5090	   0	   0	        0	  119	 false
chr1 	   2228809	 C       	  38104	      2	  34457	      0	      4	  3641	   0	   0	        0	  119	 false
chr1 	   2228810	 C       	  38400	      2	  34764	      0	      6	  3628	   1	   0	        0	  119	 false
chr1 	   2228811	 G       	  38413	     18	      1	  23571	      1	 14817	   0	   5	        0	  119	 false
chr1 	   2228812	 G       	  38541	      2	      0	  33592	      0	  4947	   0	   0	        0	  119	 false

Could you comment on whether if this in intentional?

Thanks!

[sstadick]

Hello! Yes, N's are counted toward the depth. That is intentional and the docs should be updated to reflect that.

[sstadick]

Docs update coming in 1.0 release: #84