my $command = "java -jar $picard/MergeSamFiles.jar INPUT= $files_bam OUTPUT=$sample_name" . "-tmp-herc2.bam MERGE_SEQUENCE_DICTIONARIES=TRUE CREATE_INDEX=TRUE";
system($command);

my $command = "java -jar $picard/MarkDuplicates.jar INPUT=$sample_name-tmp-herc2.bam OUTPUT=$sample_name-herc2.bam METRICS_FILE=tmp REMOVE_DUPLICATES=TRUE CREATE_INDEX=TRUE";
system($command);

unlink "$sample_name-tmp-herc2.bam";
unlink "$sample_name-tmp-herc2.bai";
unlink "tmp";