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Old 08-12-2011, 01:49 PM   #1
oiiio
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Default understanding dwgsim_eval output

Here is the command line:

Code:
dwgsim_eval -b -g 0 1300000.bwa.01.sorted.bam
Here is the first line of the output:
Code:
60           13 / 2111834                 13       2111834       2600004  6.156e-06  6.156e-06  5.000e-06  5.000e-06
There were 1300002 pairs so a total of 2600004. I read what information was on the dwgsim website, but I am still having trouble understanding how to read this output. Any help/comments/input at all would be greatly appreciated.
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Old 08-12-2011, 07:16 PM   #2
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I would be happy to explain given specific questions, and then update the documentation: http://sourceforge.net/apps/mediawik..._-_dwgsim_eval
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Old 08-15-2011, 10:50 AM   #3
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Thanks, and for starters does the 13 / 2111834 indicate that 13 out of 2111834 reads mapped correctly at that threshold? The second column ('mc' on the documentation) indicates this, correct?
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Old 08-15-2011, 10:53 AM   #4
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Could you print the line in question?
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Old 08-15-2011, 01:23 PM   #5
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Code:
60           13 / 2111834                 13       2111834       2600004  6.156e-06  6.156e-06  5.000e-06  5.000e-06
Here is the line in question from my output.
The only thing that I understand for sure is that 60 in the first column is the minimum mapping quality threshold. The documentation indicates 19 columns in the output, whereas I have only 9. Maybe some columns are showing null values?

This might be asking a bit much, but could you tell me the meanings of '13/2111834' , '13' , '2111834', and '2600004'? Perhaps that could help me understand what is happening here.

Again, i used parameters '-g 0' and '-b' for BWA.

Last edited by oiiio; 08-15-2011 at 01:25 PM. Reason: more details
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Old 08-15-2011, 01:34 PM   #6
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I think you have an old version. I released a dwgsim package update yesterday.

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Old 08-15-2011, 02:04 PM   #7
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Code:
In function "process_bam": Warning[OutOfRange]. Variable/Value: 2L 17664817 17664105 1 0 4 0 0 2 0 0 116ac.
Message: [dwgsim_eval] read was not generated by dwgsim?.
Does the new version of dwgsim_eval require that reads were generated by the newer version of dwgsim ?
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Old 08-15-2011, 02:26 PM   #8
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Yes it does unfortunately. Those two are intimately paired. Also, you can subscribe to dnaa-help@lists.sourceforge.net to get notified with updates.
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Old 08-15-2011, 02:36 PM   #9
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Are there any errors in the old versions of dwgsim and _eval? I wanted to verify results from my own BAM parser that I am using on dwgsim data.

If possible do you think you could help me understand what I am seeing in my output from the old version?
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Old 08-15-2011, 02:44 PM   #10
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Sure, could you give me the version #? You might be able to get it when you run dwgsim without any options.
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Old 08-15-2011, 03:32 PM   #11
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The version is 0.1.2
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Old 08-15-2011, 03:42 PM   #12
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Caveat: I really like the new version a lot better, and there may be bugs in the old version. Below are the columns:
#1: metric
#2: # mapped correctly at the threshold
#3: # of mapped at the threshold
#4: # mapped correctly at or greater than the threshold
#5: # of mapped at or greater than the threshold
#6: # of reads total
#7: fraction of reads mapped correctly of those mapped, at the threshold
#8: fraction of reads mapped correctly of those mapped, at or greater than the threshold
#9: fraction of reads mapped correctly out of all reads, at the threshold
#10: fraction of reads mapped correctly out of all reads, at or greater than the threshold
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Old 08-15-2011, 04:10 PM   #13
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Awesome, thanks. I will upgrade to the newer version, but for now I have a ton of data that was generated with my older one.
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