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Mpileup Variant Call

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
• 5,504 views • link
updated by lh3 lh3 • written by Tiffani • Tiffani

2 answers

Email to the samtools mailing list:

[?]

• 1 views • link
written by lh3 lh3

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
• 4 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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

• 0 views • link
written by Tiffani • Tiffani

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

• 0 views • link
written by Dan Dan

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