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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
*[[C++ Executable: bam#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
*[[C++ Executable: bam#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
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
**Genotype concordance based detection
**Estimate based on population allele frequencies without genotype data
==== Update the File ====
==== Update the File ====
==SAM/BAM==
==SAM/BAM==
*Recalibrator – Resource-efficient tool, which recalibrates base qualities based on an adaptive logistic regression model - <span style="color:#D2691E">Available upon request</span>
*Recalibrator – Resource-efficient tool, which recalibrates base qualities based on an adaptive logistic regression model - <span style="color:#D2691E">Available upon request</span>
*Deduper – Mark or remove duplicates - <span style="color:#D2691E">Coming Soon</span>
*Deduper – Mark or remove duplicates - <span style="color:#D2691E">Coming Soon</span>
