[sklages]

If you have an ACE file from MOSAIK, you should have the original (sorted) alignment from MOSAIK, which you can easily use to create a BAM file with MosaikText,

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MosaikText 1.0.1388 2010-02-01
Michael Stromberg Marth Lab, Boston College Biology Department
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Description: exports reads and alignments from MOSAIK.

Usage: MosaikText -in <filename> -out <filename> -ia <filename>

Read Archive Options:
-ir <MOSAIK read filename> the input read file
-fastq <FASTQ filename> stores the data in a FASTQ file
-screen displays the reads on the screen

Alignment Archive Options:
-in <MOSAIK alignment filename> the input alignment file
-axt <axt filename> stores the data in an AXT file
-bam <bam filename> stores the data in a BAM file
-bed <bed filename> stores the data in a BED file
-eland <eland filename> stores the data in an Eland file
-ref <reference sequence name> displays output for a specific reference
-sam <sam filename> stores the data in a SAM file
-screen displays the alignments on the screen
-u limit output to unique reads

$ MosaikText -in PROJ_sorted.dat -bam PROJ.bam

Then use samtools or whatever you want :-)