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Old 11-16-2015, 12:56 PM   #6
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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Map to the reference with BBMap, like this:

bbmap.sh ref=reference.fa in=reads.fq out=mapped.sam mhist=mhist.txt ehist=ehist.txt qhist=qhist.txt indelhist=indelhist.txt

BBMap will print useful statistics to the screen:
Code:
Read 1 data:            pct reads       num reads       pct bases          num bases

mapped:                  99.6100%            9961        99.6100%            1494150
unambiguous:             97.8900%            9789        97.8900%            1468350
ambiguous:                1.7200%             172         1.7200%              25800
low-Q discards:           0.0000%               0         0.0000%                  0

perfect best site:        1.7500%             175         1.7500%              26250
semiperfect site:         1.7500%             175         1.7500%              26250

Match Rate:                   NA               NA        61.1359%            1409105
Error Rate:              96.0596%            9605        38.5408%             888317
Sub Rate:                87.2787%            8727         2.2734%              52398
Del Rate:                43.4543%            4345        35.1743%             810722
Ins Rate:                48.9249%            4892         1.0932%              25197
N Rate:                  50.2050%            5020         0.3232%               7450
....and you can also plot the mhist or other histograms, for more details.

Quote:
Originally Posted by skbrimer View Post
Also why would it be bad to error correct in those situations, I imagine that it will have to due with "correcting" away an actual variant but a variant would still have to be present at a rate higher than the machine's error rate to be called with an confidance right? i.e. if you have a 1% error rate and 1000x coverage you could not call anything less than 10X right?
Error correction relies on high depth. With low depth it just doesn't work, and low depth of a variant compared to the reference will lead to that variant getting corrected away.

Last edited by Brian Bushnell; 11-16-2015 at 12:58 PM.
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