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  1. A CyVerse account. (Register for an CyVerse account here -
  2. Mandatory arguments 
    1. Input directory: Directory of SAM/BAM files to analyze. The alignment files must be coordinate sorted. 
  3. Optional arguments:
    1. VALIDATION_STRINGENCY: Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: LENIENT. This option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, SILENT}
    2. REMOVE_DUPLICATES: If true do not write duplicates to the output file instead of writing them with appropriate flags set. Default value: true.



Sample data

The following test data are provided for testing BWA-index-mem here /iplant/home/xiaofei_iplant/Sorghum_chr8/chr8_test:

  1.  BWA-index-mem_0.7.10_Apr10_Test/G3_P_H3_chr8_BWA_bam and BWA-index-mem_0.7.10_Apr10_Test//G3_P_K4me3_chr8_BWA_bam (output bam 
    Note: These are the outputs of BWA-index-mem_0.7.10).


Successful execution of the Picard_MarkDup_2.7.0 will create 2 directories named out for BAM files and metrics. 



  1. BAM files
    1. G3_P_H3_rep1_chr8_rmDup.sorted.bam
    2. G3_P_H3_rep1_chr8_rmDup.sorted.bam.bai
    3. G3_P_H3_rep2_chr8_rmDup.sorted.bam
    4. G3_P_H3_rep2_chr8_rmDup.sorted.bam.bai
    1. G3_P_K4me3_rep1_chr8_rmDup.sorted.bam
    2. G3_P_K4me3_rep1_chr8_rmDup.sorted.bam.bai
    3. G3_P_K4me3_rep2_chr8_rmDup.sorted.bam
    4. G3_P_K4me3_rep2_chr8_rmDup.sorted.bam.bai
  2. Metrics files
    1. G3_P_H3_rep1_chr8_rmDup_metrics.txt
    2. G3_P_H3_rep2_chr8_rmDup_metrics.txt
    1. G3_P_K4me3_rep1_chr8_rmDup_metrics.txt
    2. G3_P_K4me3_rep2_chr8_rmDup_metrics.txt