Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

mpileup loses bases of alignments starting with a insertion #139

Open
alumi opened this issue Aug 10, 2018 · 0 comments
Open

mpileup loses bases of alignments starting with a insertion #139

alumi opened this issue Aug 10, 2018 · 0 comments

Comments

@alumi
Copy link
Member

alumi commented Aug 10, 2018

input SAM

@SQ	SN:ref	LN:45
q001	0	ref	10	60	4I4M4D4M4I	*	0	0	ATGCATGCATGCATGC	ABCDEFGHIJKLMNOP

samtools output

ref	10	N	1	^]A	E
ref	11	N	1	T	F
ref	12	N	1	G	G
ref	13	N	1	C-4NNNN	H
ref	14	N	1	*	I
ref	15	N	1	*	I
ref	16	N	1	*	I
ref	17	N	1	*	I
ref	18	N	1	A	I
ref	19	N	1	T	J
ref	20	N	1	G	K
ref	21	N	1	C+4ATGC$	L

cljam output

ref	10	N	1	^]A	E
ref	11	N	1	T	F
ref	12	N	1	G	G
ref	13	N	1	C-4NNNN	H
ref	14	N	1	*	~
ref	15	N	1	*	~
ref	16	N	1	*	~
ref	17	N	1	*	~
ref	18	N	1	A	I
ref	19	N	1	T	J
ref	20	N	1	G	K
ref	21	N	1	C+4ATGC$	L
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant