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BamUtil: polishBam (view source)

Revision as of 16:21, 1 November 2010

3,542 bytes added ,  16:21, 1 November 2010
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Returns 0.
 
Returns 0.
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=== Example Output ===
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=== Example ===
 +
Command:
 
<pre>
 
<pre>
 +
../../bin/polishBam  --in testFiles/sortedSam.sam --out results/updatedSam.sam --log results/updated.log --checkSQ --fasta testFiles/testFasta.fa --AS my37 --UR testFasta.fa --RG "@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA" --PG "@PG ID:polish VN:0.0.1" --SP new --HD "@HD VN:1.0 SO:coordinate GO:none"
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</pre>
 +
 +
Input File:
 +
<pre>
 +
@SQ SN:1 LN:2004
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@SQ SN:2 LN:2000
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@SQ SN:3 LN:2005
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@SQ SN:4 LN:2040
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@SQ SN:5 LN:2006
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@RG ID:myID LB:library SM:sample
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@RG ID:myID2 SM:sample2 LB:library2
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@CO Comment 1
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@CO Comment 2
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18:462+29M5I3M:F:295 97 1 75 0 5M 18 757 0 ACGTN ;>>>> AM:i:0 MD:Z:30A0C5 NM:i:2 XT:A:R
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18:462+29M5I3M:F:295 97 1 75 0 * 18 757 0 * * AM:i:0
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1:1011:F:255+17M15D20M 73 1 1011 0 5M2D = 1011 0 CCGAA 6>6+4 AM:i:0 MD:Z:37 NM:i:0 XT:A:R
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1:1011:F:255+17M15D20M 133 1 1012 0 * = 1011 0 CTGT >>9>
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18:462+29M5I3M:F:296 97 1 1751 0 3S2H5M 18 757 0 TGCACGTN 453;>>>>
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18:462+29M5I3M:F:295 97 2 75 0 5M 18 757 0 ACGTN * AM:i:0 MD:Z:30A0C5 NM:i:2 XT:A:R
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18:462+29M5I3M:F:297 97 2 1751 0 3S5M1S3H 18 757 0 TGCACGTNG 453;>>>>5
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18:462+29M5I3M:F:298 97 3 75 0 3S5M4H 18 757 0 TGCACGTN 453;>>>>
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Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 AACT ==;;
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Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 * *
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</pre>
 +
 +
 +
Output File:
 +
<pre>
 +
@SQ SN:1 LN:2004 AS:my37 M5:a9cfe5b8c11aa0cc2c0d2bf3602c9804 UR:testFasta.fa SP:new
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@SQ SN:2 LN:2000 AS:my37 M5:7c342606b54aa211a50f5f63ac1cb2eb UR:testFasta.fa SP:new
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@SQ SN:3 LN:2005 AS:my37 M5:c30e547093f33de240b164a4a2ebe3b5 UR:testFasta.fa SP:new
 +
@SQ SN:4 LN:2040 AS:my37 M5:fc4c559e9da51e93e7875031ddf65f2a UR:testFasta.fa SP:new
 +
@SQ SN:5 LN:2006 AS:my37 M5:c876194283debb8b507ebd0f82309ec4 UR:testFasta.fa SP:new
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@RG ID:myID LB:library SM:sample
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@RG ID:myID2 SM:sample2 LB:library2
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@HD VN:1.0 SO:coordinate GO:none
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@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA
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@PG ID:polish VN:0.0.1
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@CO Comment 1
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@CO Comment 2
 +
18:462+29M5I3M:F:295 97 1 75 0 5M 18 757 0 ACGTN ;>>>> AM:i:0 MD:Z:30A0C5 NM:i:2 RG:Z:UM0037:1 XT:A:R
 +
18:462+29M5I3M:F:295 97 1 75 0 * 18 757 0 * * AM:i:0 RG:Z:UM0037:1
 +
1:1011:F:255+17M15D20M 73 1 1011 0 5M2D = 1011 0 CCGAA 6>6+4 AM:i:0 MD:Z:37 NM:i:0 RG:Z:UM0037:1 XT:A:R
 +
1:1011:F:255+17M15D20M 133 1 1012 0 * = 1011 0 CTGT >>9> RG:Z:UM0037:1
 +
18:462+29M5I3M:F:296 97 1 1751 0 3S2H5M 18 757 0 TGCACGTN 453;>>>> RG:Z:UM0037:1
 +
18:462+29M5I3M:F:295 97 2 75 0 5M 18 757 0 ACGTN * AM:i:0 MD:Z:30A0C5 NM:i:2 RG:Z:UM0037:1 XT:A:R
 +
18:462+29M5I3M:F:297 97 2 1751 0 3S5M1S3H 18 757 0 TGCACGTNG 453;>>>>5 RG:Z:UM0037:1
 +
18:462+29M5I3M:F:298 97 3 75 0 3S5M4H 18 757 0 TGCACGTN 453;>>>> RG:Z:UM0037:1
 +
Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 AACT ==;; RG:Z:UM0037:1
 +
Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 * * RG:Z:UM0037:1
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</pre>
 +
 +
Output:
 +
<pre>
 +
in testFiles/sortedSam.sam
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out results/updatedSam.sam
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log results/updated.log
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checkSQ
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</pre>
 +
 +
Log File:
 +
<pre>
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Arguments in effect:
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--in [testFiles/sortedSam.sam]
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--out [results/updatedSam.sam]
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--log [results/updated.log]
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--fasta [testFiles/testFasta.fa]
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--AS [my37]
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--UR [testFasta.fa]
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--SP [new]
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--checkSQ [ON]
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--HD [@HD VN:1.0 SO:coordinate GO:none]
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--RG [@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA]
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--PG [@PG ID:polish VN:0.0.1]
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Reading the reference file testFiles/testFasta.fa
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Finished reading the reference file testFiles/testFasta.fa
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Finished checking the consistency of SQ tags
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Creating the header of new output file
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Adding 1 HD, 1 RG, and 1 PG headers
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Finished writing output headers
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Writing output BAM file
 +
Successfully written 10 records
 
</pre>
 
</pre>
  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/2339"

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