Mismatch

Angsd can output mismatch from the reference given:

- Distance from be beginning of the read (posi)

- Distance from the end of the read (isop)

- Strand

- Qscore

Run like:

./angsd -i my.cram -ref hg19.fa -doMisMatch 1

Output looks like:

posi	isop	qs	strand	Ref	A	C	G	T
0	24	13	0	1	0	2	0	0
0	24	13	0	3	0	0	0	1
0	24	13	1	0	1	0	0	0
0	24	13	1	3	0	0	0	1
0	24	14	0	0	152	1	4	0
0	24	14	0	1	0	128	0	0
0	24	14	0	2	11	2	196	1
0	24	14	0	3	1	0	2	12
0	24	14	1	0	20	1	2	2
0	24	14	1	1	1	200	1	16
0	24	14	1	2	0	5	118	6
0	24	14	1	3	0	6	3	164
0	24	15	0	0	186	1	2	0
0	24	15	0	1	4	91	0	0
0	24	15	0	2	8	0	90	0
0	24	15	0	3	0	1	2	7
0	24	15	1	0	14	1	0	0
0	24	15	1	1	0	93	1	2
0	24	15	1	2	0	2	79	2