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annotate sort_bam.sh @ 20:ea52ef8d7f3a

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added perl dependency since galaxy A seems working and added samtools sort
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 19:17:11 -0400
parents
children cf0d2b74769e
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20
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
1 #!/bin/bash
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
2 results=$1;
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
3 bam_file=$2;
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
4
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
5 samtools sort $bam_file $results 2>log.txt
ea52ef8d7f3a added perl dependency since galaxy A seems working and added samtools sort
biomonika <biomonika@psu.edu>
parents:
diff changeset
6