my $command = "java -jar $picard/MergeSamFiles.jar INPUT=HG00119.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam
INPUT=HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam OUTPUT=HG00119" . "-tmp-herc2.bam MERGE_SEQUENCE_DICTIONARIES=TRUE CREATE_INDEX=TRUE";
system($command);
my $command = "java -jar $picard/MarkDuplicates.jar INPUT=HG00119-tmp-herc2.bam OUTPUT=HG00119-herc2.bam METRICS_FILE=tmp REMOVE_DUPLICATES=TRUE CREATE_INDEX=TRUE";
system($command);
    
unlink "HG00119-tmp-herc2.bam";
unlink "HG00119-tmp-herc2.bai";
unlink "tmp";