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408 bytes added
, 15:58, 30 September 2010
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| Steps: | | Steps: |
| # Run this program and pipe it into samtools sort by query name | | # 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.bam</pre> | + | #* <pre>./bam filter --in <your InputFile> --refFile <your reference file> --out -.bam <any other options> | samtools sort -n - tempQuerySort</pre> |
| # Run samtools fixmate and pipe it into samtools sort by position | | # Run samtools fixmate and pipe it into samtools sort by position |
− | #* <pre></pre> | + | #* <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 === | | === Parameters === |
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| | | |
| Input Parameters | | Input Parameters |
− | --in [testFiles/testFilter.sam], --out [-], | + | --in [../../originalBamFile.bam], |
− | --refFile [testFiles/chr1_partial.fa], --noeof, --qualityThreshold [30],
| + | --out [-.bam], --refFile [/home/mktrost/data/human.g1k.v37.fa], --noeof, |
− | --defaultQualityInt [20], --mismatchThreshold [0.49]
| + | --qualityThreshold [60], --defaultQualityInt [20], --mismatchThreshold [0.10] |
| | | |
− | open and prefetch reference genome testFiles/chr1_partial.fa: done. | + | open and prefetch reference genome /home/mktrost/data/human.g1k.v37.fa: done. |
− | Number of Reads Clipped by Filtering: 8 | + | Number of Reads Clipped by Filtering: 704578 |
− | Number of Reads Filtered Due to MismatchThreshold: 1 | + | Number of Reads Filtered Due to MismatchThreshold: 0 |
− | Number of Reads Filtered Due to QualityThreshold: 2 | + | Number of Reads Filtered Due to QualityThreshold: 13064 |
| + | [bam_sort_core] merging from 3 files... |
| + | [bam_sort_core] merging from 3 files... |
| </pre> | | </pre> |