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*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
*[[BamUtil: readIndexedBam|ReadIndexedBam]] - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file
*[[BamUtil: readIndexedBam|ReadIndexedBam]] - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file
*[[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files
==== Update the File ====
==== Update the File ====
