SAMtools pileup output

[zippered_ohio]

Hi all,

I have used SAMtools pileup in order to identify indels. According to this page, there should be 13 columns.

My output has 15 columns, and most of the lines make sense, e.g.:

chr1	107591963	*	*/-TC	69	69	59	91	*	-TC	86	5	0	0	0

I assumed that the sum of columns 11, 12, and 13 would equal column 8. This holds for most of the indels, but I noticed it doesn't hold for all.

There are certain regions with very high read depths and which do not satisfy (c11+c12+c13)==c8. Example:

chr2	98507236	*	*/*	2652	0	28	7999	*	-T	1019	5	0	0	0
chr2	98507238	*	*/*	2619	0	28	8001	*	-G	1022	1	1	1	964
chr2	98507239	*	*/*	2800	0	28	8000	*	-A	1017	6	1	0	0
chr2	98507245	*	*/*	2947	0	28	7990	*	-G	1022	2	0	0	0
chr2	98507247	*	*/*	2990	0	29	7998	*	-C	1021	3	0	0	0
chr2	98507249	*	*/*	3016	0	29	7992	*	-A	1023	1	0	0	0

When I view this region in IGV (screenshot), it looks poorly mapped but definitely not read depths of ~10k.

Any ideas on why this might be?

[nilshomer]

Pileup is no longer in the new release, try using "mpileup" as you will have trouble be finding support.