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new injector args and address Kiran's question 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1134 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2009-06-30 19:49:22 +00:00
parent 8d3dc57c3d
commit fdff233d70
1 changed files with 2 additions and 2 deletions
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4
doc/MSA_Realigner_README.txt
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@ -76,6 +76,7 @@ Step 2: Merging the intervals
At this point, you need to combine any intervals files you have into a
master list; this is done by running the interval merger.
*** Note that this step needs to be done even if you have only a single intervals file.
Usage: java -jar dist/GenomeAnalysisTK.jar -I <input.bam> -R <ref.fasta> -T IntervalMerger
--intervalsToMerge intervalsOutput1.txt [--intervalsToMerge intervalsOutput2.txt]
@ -130,8 +131,7 @@ Important note: this option works best with the
First, be sure to index your cleaned output BAM from Step 3:
samtools index <output.bam>
Usage: java -jar dist/GenomeAnalysisTK.jar -I <originalInput.bam> -R <ref.fasta> -T CleanedReadInjector
--cleaned_intervals mergedIntervalList.txt --cleaned_reads <previousOutput.bam> -S SILENT --output_bam <fullOutput.bam>
Usage: java -jar dist/GenomeAnalysisTK.jar -I <originalInput.bam> -R <ref.fasta> -T CleanedReadInjector --cleaned_reads <previousOutput.bam> -S SILENT --output_bam <fullOutput.bam>
Optional Arguments:
--bam_compression N [when used with OutputCleaned it determines the BAM compression; default=5, recommended=1]