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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.
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:
