HG00119.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam
HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam
HG00117.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam
HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam
HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam_herc2_phase1.bam
NA20828.mapped.illumina.mosaik.TSI.exome.20110411.bam_herc2_phase1.bam
NA20828.mapped.ILLUMINA.bwa.TSI.low_coverage.20130415.bam_herc2_data.bam
NA20828.mapped.ILLUMINA.bwa.TSI.low_coverage.20101123.bam_herc2_phase1.bam
NA20828.mapped.ILLUMINA.bwa.TSI.exome.20121211.bam_herc2_data.bam

##</code><code>##

HG00119
HG00117
NA20828

##</code><code>##

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";

##</code><code>##

%files = (
    'HG00119' => ['HG00119.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam',  'HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam'],
    'HG00117' => ['HG00117.mapped.illumina.mosaik.GBR.exome.20110411.bam_herc2_phase1.bam', 'HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam_herc2_data.bam', 'HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam_herc2_phase1.bam'],
);

##</code><code>##

my %hash;

$hash{$_} = [ glob("$_*.bam") ] for @lines;

##</code><code>##

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";