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, 15:51, 30 September 2010
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| The <code>filter</code> option on the [[Bam|bam executable]] writes the alignments filtering them by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high. | | The <code>filter</code> option on the [[Bam|bam executable]] writes the alignments filtering them by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high. |
| | | |
| + | The following modifications may occur in an alignment: |
| + | * CIGAR updated to reflect clips |
| + | * POS updated to reflect a new CIGAR if clipping occurs at the front of a read |
| + | * FLAG updated to reflect a read is unmapped if it is below the quality of mismatches is too high, or clipping would cause an entire read to be clipped. |
| + | |
| + | === NOTES === |
| + | The POS and FLAG fields of an alignment are reflected in the mate's alignment. Thus, when the mate also needs to be updated. |
| + | |
| + | Also, if the file was sorted, and a POS was changed, the file may no longer be sorted. |
| + | |
| + | '''NOTE: This program does NOT update the mate or resort the file.''' |
| + | |
| + | In order to update the mate, samtools fixmate must be run. |
| + | |
| + | In order to reorder the file, samtools sort must be run. |
| + | |
| + | Notes about the samtools programs: |
| + | * samtools fixmate requires the file to be sorted by query name. |
| + | * samtools sort cannot write to pipes. |
| + | |
| + | 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.bam</pre> |
| + | # Run samtools fixmate and pipe it into samtools sort by position |
| + | #* <pre></pre> |
| | | |
| === Parameters === | | === Parameters === |