Question

Mpileup Variant Call

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13.4 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 • 4.9k views

ADD COMMENT • link updated 13.4 years ago by lh3 33k • written 13.4 years ago by Tiffani ▴ 150

score 6 · Answer 1 · 2011-07-08

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13.4 years ago

lh3 33k

Email to the samtools mailing list:

[?]

ADD COMMENT • link 13.4 years ago by lh3 33k

Ram · Answer 2 · 2011-07-08

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13.4 years ago

Pierre Lindenbaum 164k

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 • link updated 5.2 years ago by Ram 44k • written 13.4 years ago by Pierre Lindenbaum 164k

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

ADD REPLY • link 13.4 years ago by Tiffani ▴ 150

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

ADD REPLY • link 11.8 years ago by Dan ▴ 540