Mercurial > repos > kyost > atac_primer_tool

diff filter_bam.bash @ 5:3cd53127a838 draft default tip

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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author kyost
date Fri, 04 May 2018 02:24:47 -0400
parents fd3ea97a96bc
children
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line diff
--- a/filter_bam.bash	Wed May 02 13:20:21 2018 -0400
+++ b/filter_bam.bash	Fri May 04 02:24:47 2018 -0400
@@ -29,7 +29,7 @@
 
 #create bed file of fragments for each bam file
 
-samtools view -b -L $ext_peak_file $bam_file > $filtered_bam_file
+samtools view -b -F 4 -L $ext_peak_file $bam_file > $filtered_bam_file
 
 rm name
 rm count