From Genome Analysis Wiki
Jump to navigationJump to search
23 bytes added
, 13:16, 13 June 2011
Line 383: |
Line 383: |
| </pre> | | </pre> |
| | | |
− | ==== Bam Format ==== | + | ==== SAM/Bam Format ==== |
− | use .bam extension to output in BAM format instead of diff format. | + | use .sam/.bam extension to output in SAM/BAM format instead of diff format. |
| | | |
− | In 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>.bam with records only in the in1 file | + | # specified name with _only_<in1>.b(s)am with records only in the in1 file |
− | # specified name with _only_<in2>.bam with records only in the in2 file | + | # specified name with _only_<in2>.b(s)am 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: |