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, 13:17, 13 June 2011
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| --in2 : second coordinate sorted SAM/BAM file to be diffed | | --in2 : second coordinate sorted SAM/BAM file to be diffed |
| Optional Parameters: | | Optional Parameters: |
− | --out : output filename, use .bam extension to output in BAM format instead of diff format. | + | --out : output filename, use .bam extension to output in SAM/BAM format instead of diff format. |
− | In BAM format there will be 3 output files: | + | In SAMBAM format there will be 3 output files: |
| 1) the specified name with record diffs | | 1) the specified name with record diffs |
− | 2) specified name with _only_<in1>.bam with records only in the in1 file | + | 2) specified name with _only_<in1>.sam/bam with records only in the in1 file |
− | 3) specified name with _only_<in2>.bam with records only in the in2 file | + | 3) specified name with _only_<in2>.sam/bam with records only in the in2 file |
| --seq : diff the sequence bases. | | --seq : diff the sequence bases. |
| --baseQual : diff the base qualities. | | --baseQual : diff the base qualities. |
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| In SAM/BAM format there will be 3 output files: | | In SAM/BAM format there will be 3 output files: |
| # the specified name with record diffs | | # the specified name with record diffs |
− | # specified name with _only_<in1>.b(s)am with records only in the in1 file | + | # specified name with _only_<in1>.sam/bam with records only in the in1 file |
− | # specified name with _only_<in2>.b(s)am with records only in the in2 file | + | # specified name with _only_<in2>.sam/bam with records only in the in2 file |
| | | |
| When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags: | | When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags: |