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BamUtil: filter

408 bytes added, 14:58, 30 September 2010
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Steps:
# Run this program and pipe it into samtools sort by query name
#* <pre>./bam filter --in <your InputFile> --refFile <your reference file> --out -.bam <any other options> | samtools sort -n - temp.bamtempQuerySort</pre>
# Run samtools fixmate and pipe it into samtools sort by position
#* <pre>samtools fixmate tempQuerySort.bam - | samtools sort - finalResult</pre> For Example: ~/pipeFilter/bam/bam filter --in ../../originalBamFile.bam --refFile ~/data/human.g1k.v37.fa --out -.bam | samtools sort -n - tempQuerySort; samtools fixmate tempQuerySort.bam - | samtools sort - newResult 
=== Parameters ===
Input Parameters
--in [testFiles../../testFilteroriginalBamFile.sambam], --out [-.bam], --refFile [testFiles/chr1_partialhome/mktrost/data/human.g1k.v37.fa], --noeof, --qualityThreshold [3060], --defaultQualityInt [20], --mismatchThreshold [0.4910]
open and prefetch reference genome testFiles/chr1_partialhome/mktrost/data/human.g1k.v37.fa: done.Number of Reads Clipped by Filtering: 8704578Number of Reads Filtered Due to MismatchThreshold: 10Number of Reads Filtered Due to QualityThreshold: 213064[bam_sort_core] merging from 3 files...[bam_sort_core] merging from 3 files...
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