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, 11:49, 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. |
| + | In BAM format there will be 3 output files: |
| + | 1) the specified name with record diffs |
| + | 2) specified name with _only_<in1>.bam with records only in the in1 file |
| + | 3) specified name with _only_<in2>.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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| | | |
| === Output Format === | | === Output Format === |
| + | 2 Output Formats: |
| + | # Diff Format |
| + | # BAM Format |
| + | |
| + | ==== Diff Format ==== |
| There are 2 types of differences. | | There are 2 types of differences. |
| * ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff | | * ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff |
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| If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3. | | If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3. |
| | | |
− | ==== Example Output ==== | + | ===== Example Output ===== |
| Command: | | Command: |
| ../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs --out results/diffOrderSam.log | | ../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs --out results/diffOrderSam.log |
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| DEF | | DEF |
| > cd *:0 * * * | | > cd *:0 * * * |
| + | |
| + | ==== Bam Format ==== |
| + | use .bam extension to output in BAM format instead of diff format. |
| + | |
| + | In BAM format there will be 3 output files: |
| + | # the specified name with record diffs |
| + | # specified name with _only_<in1>.bam with records only in the in1 file |
| + | # specified name with _only_<in2>.bam with records only in the in2 file |
| | | |
| == readReference == | | == readReference == |