Select Code to Download

Select or download this

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

Select or download this
```
HG00119
HG00117
NA20828
```

Select or download this

my $command = "java -jar $picard/MergeSamFiles.jar INPUT= $files_bam O
+UTPUT=$sample_name" . "-tmp-herc2.bam MERGE_SEQUENCE_DICTIONARIES=TRU
+E CREATE_INDEX=TRUE";
system($command);
...
unlink "$sample_name-tmp-herc2.bam";
unlink "$sample_name-tmp-herc2.bai";
unlink "tmp";

Select or download this

%files = (
    'HG00119' => ['HG00119.mapped.illumina.mosaik.GBR.exome.20110411.b
+am_herc2_phase1.bam',  'HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.
+20120522.bam_herc2_data.bam'],
    'HG00117' => ['HG00117.mapped.illumina.mosaik.GBR.exome.20110411.b
+am_herc2_phase1.bam', 'HG00117.mapped.ILLUMINA.bwa.GBR.low_coverage.2
+0120522.bam_herc2_data.bam', 'HG00117.mapped.ILLUMINA.bwa.GBR.low_cov
+erage.20101123.bam_herc2_phase1.bam'],
);

Select or download this

my %hash;

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

Select or download this

my $command = "java -jar $picard/MergeSamFiles.jar INPUT=HG00119.mappe
+d.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_DICTIONARIE
+S=TRUE CREATE_INDEX=TRUE";
...
unlink "HG00119-tmp-herc2.bam";
unlink "HG00119-tmp-herc2.bai";
unlink "tmp";