Originally posted by NextGenSeb
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Fair enough, maybe that gives me teh motivation to finally improve my almost non-existent python skills
Got a few more questions fo ryou though:
1. The "bed-like" format for candidate mutations (-b option), what is that supposed to look like? From the header files the first three columns are pretty clear, but I am stuck with regards to the mutation type and the rest of the file
2. Still in reagards to mutations, is there a way to simulate specific mutation frequencies? I would like like to test aligners and variant callers for somatic mutations and hence need a degree of frequency control over the inserted mutations.
3. The IonTorrent homopolymer errors (elegedly) got better with the new chemistry. Is there a way to potentially adjust the error frequencies in the program for this?
Thanks for the quick reply and your comments.
Cheers
Seb
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Originally posted by NextGenSeb View PostFair enough, maybe that gives me teh motivation to finally improve my almost non-existent python skills
Got a few more questions fo ryou though:
Originally posted by NextGenSeb View Post1. The "bed-like" format for candidate mutations (-b option), what is that supposed to look like? From the header files the first three columns are pretty clear, but I am stuck with regards to the mutation type and the rest of the file
Originally posted by NextGenSeb View Post2. Still in reagards to mutations, is there a way to simulate specific mutation frequencies? I would like like to test aligners and variant callers for somatic mutations and hence need a degree of frequency control over the inserted mutations.
Originally posted by NextGenSeb View Post3. The IonTorrent homopolymer errors (elegedly) got better with the new chemistry. Is there a way to potentially adjust the error frequencies in the program for this?
Seb
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Originally posted by chintanspy View PostHi Nils,
what parameters are used for placing a read under 'mi' category?
After observing the results, not all the reads which map at different co-ordinate than simulated position are categorized under 'mi'.
It can also be affected by the "-g" parameter.
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Originally posted by plantae View PostI was confused by "-d" opinition
NB: the -d option was previously incorrectly stated as being the outer distance, but is in fact the inner distance.
for a PE-read
5--->3______3<---5
"-d" means for distance between 3' and 3' of the PE reads?
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Originally posted by nilshomer View PostSee the help message for the latest version.
-d INT inner distance between the two ends [500]
"the two ends"
means for two pair-end reads?
or 3' end of two pair-end reads?
or 5' end of two pair-end reads?
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I have used dwgsim 0.1.10 to generate reads from hg19 chromosome 22, and tested the sensitivities of variant callers SAMtools, GATK, and glfSingle.
The default per base error rate 0.02 is used.
Even up to 100X ('-C 100' in simulation), GATK and glfSingle can identify only 86% the the variants. But SAMtools can call 95%.
Shall I reduce the error rate?
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