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BamUtil: polishBam (view source)

Revision as of 14:06, 6 January 2014

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== Trim BAM ==
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= Overview of the <code>polishBam</code> function of <code>bamUtil</code> =
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The <code>trimBam</code> program is released as part of the StatGen Library & Tools download.
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The <code>polishBam</code> option on the [[bamUtil]] executable adds/updates header lines & adds the RG tag to each record.
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<code>trimBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
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= Usage =
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./bam polishBam (options) --in <inBamFile> --out <outBamFile>
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= Parameters =
 +
<pre>
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  Required parameters:
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        -i/--in : input BAM file
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        -o/--out : output BAM file
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  Optional parameters:
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        -v : turn on verbose mode
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        -l/--log : writes logfile. <outBamFile>.log will be used if value is unspecified
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        --HD : add @HD header line
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        --RG : add @RG header line
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        --PG : add @PG header line
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        -f/--fasta : fasta reference file to compute MD5sums and update SQ tags
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        --AS : AS tag for genome assembly identifier
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        --UR : UR tag for @SQ tag (if different from --fasta)
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        --SP : SP tag for @SQ tag
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        --checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option
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</pre>
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{{PhoneHomeParamDesc}}
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== Required Parameters ==
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{{InBAMInputFile}}
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{{OutBAMOutputFile}}
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== Optional Parameters ==
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=== Verbose (<code>--verbose</code>) ===
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Use <code>--verbose</code> to turn on verbose mode.
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=== Specify Log Filename (<code>--log</code>) ===
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Use <code>--log</code> followed by the log filename to specify the log filename.  Default is the output file basename with a <code>.log</code> extension
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=== Add the HD Header (<code>--HD</code>) ===
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Use <code>--HD</code> followed by the HD header line to add a HD header.  Be sure to include "@HD" in the line you specify.
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=== Add the RG Header (<code>--RG</code>) ===
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Use <code>--RG</code> followed by the RG header line to add a RG header.  Be sure to include "@RG" in the line you specify.
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=== Add the PG Header (<code>--PG</code>) ===
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Use <code>--PG</code> followed by the PG header line to add a PG header.  Be sure to include "@PG" in the line you specify.
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=== Add MD5 and UR tags to SQ Headers (<code>--fasta</code>) ===
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Use <code>--fasta</code> followed by the fasta reference file name to compute MD5sums and update SQ tags with the M5 & UR values.  Use the [[#Add the UR tag to SQ Headers (--UR)|<code>--UR</code>]] option to specify a different UR value.
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=== Add the AS tag to SQ Headers (<code>--AS</code>) ===
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Use <code>--AS</code> followed by the genome assembly identify to add the AS tag to the SQ Headers.
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=== Add the UR tag to SQ Headers (<code>--UR</code>) ===
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Use <code>--UR</code> followed by the URI of the sequence to add the UR tag to the SQ Headers.
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The UR header will be automatically added with the [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]] option, so if [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]] is used, <code>--UR</code> only needs to be specified if it is different from [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]].
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=== Add the SP tag to SQ Headers (<code>--SP</code>) ===
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Use <code>--SP</code> followed by the species to add the SP tag to the SQ Headers.
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{{PhoneHomeParameters}}
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= Return Value =
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Returns 0 on success, non-0 on failure.
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=== Parameters ===
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= Example =
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Command:
 
<pre>
 
<pre>
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    Required Parameters:
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./bam 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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        inFile  : the SAM/BAM file to be read
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        outFile : the SAM/BAM file to be written
  −
        num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side
   
</pre>
 
</pre>
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=== Usage ===
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Input File:
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trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side]
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<pre>
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@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>
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=== Return Value ===
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Output File:
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Returns the SamStatus for the reads/writes.  0 on success.
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<pre>
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@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
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@SQ SN:4 LN:2040 AS:my37 M5:fc4c559e9da51e93e7875031ddf65f2a UR:testFasta.fa SP:new
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@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
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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 RG:Z:UM0037:1 XT:A:R
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18:462+29M5I3M:F:295 97 1 75 0 * 18 757 0 * * AM:i:0 RG:Z:UM0037:1
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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 RG:Z:UM0037:1 XT:A:R
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1:1011:F:255+17M15D20M 133 1 1012 0 * = 1011 0 CTGT >>9> RG:Z:UM0037:1
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18:462+29M5I3M:F:296 97 1 1751 0 3S2H5M 18 757 0 TGCACGTN 453;>>>> RG:Z:UM0037:1
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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 RG:Z:UM0037:1 XT:A:R
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18:462+29M5I3M:F:297 97 2 1751 0 3S5M1S3H 18 757 0 TGCACGTNG 453;>>>>5 RG:Z:UM0037:1
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18:462+29M5I3M:F:298 97 3 75 0 3S5M4H 18 757 0 TGCACGTN 453;>>>> RG:Z:UM0037:1
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Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 AACT ==;; RG:Z:UM0037:1
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Y:16597235+13M13I11M:F:181 141 * 0 0 * * 0 0 * * RG:Z:UM0037:1
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</pre>
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=== Example Output ===
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Output:
 
<pre>
 
<pre>
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Arguments in effect:
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in testFiles/sortedSam.sam
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Input file : testFiles/testSam.sam
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out results/updatedSam.sam
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Output file : results/trimSam.sam
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log results/updated.log
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#TrimBases : 2
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checkSQ
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</pre>
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Number of records read = 10
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Log File:
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Number of records written = 10
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<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
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Successfully written 10 records
 
</pre>
 
</pre>
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[[Category:BamUtil|polishBam]]
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[[Category:BAM Software]]
 
[[Category:Software]]
 
[[Category:Software]]
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[[Category:StatGen Download]]
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[[Category:BAM Software]]
 
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/2332...9286"

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