Mpileup Variant Call
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13.3 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
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13.3 years ago
lh3 33k

Email to the samtools mailing list:

[?]

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13.3 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
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Thanks so much! I stumbled upon those commands just now. Thank you very much!

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

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