Mpileup Variant Call
2
3
Entering edit mode
13.0 years ago
Tiffani ▴ 150

Why does mpileup call SO MANY less variants then pileup does? I know pileup is officially deprecated and doesn't even exist in the newest version of samtools that was released today, but my team needs to know WHY mpileup doesn't call as many variants.

Thanks

mpileup • 4.8k views
ADD COMMENT
6
Entering edit mode
13.0 years ago
lh3 33k

Email to the samtools mailing list:

[?]

ADD COMMENT
2
Entering edit mode
13.0 years ago

Your problem is probably the same one I had yesterday.

Why Does Mpileup Skip My Mutation ?

So, you should try to use the option

-B

or

-E
ADD COMMENT
0
Entering edit mode

Thanks so much! I stumbled upon those commands just now. Thank you very much!

ADD REPLY
0
Entering edit mode

Has anyone got true-positive / false-positive stats for all the different modes?

ADD REPLY

Login before adding your answer.

Traffic: 2165 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6