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Old 04-22-2013, 10:44 AM   #6
dietmar13
Senior Member
 
Location: Vienna

Join Date: Mar 2010
Posts: 107
Default @swbarnes

thank you, works great, but too slow with big bam files:

therefore preselection with samtools...

Code:
samtools view -b xxx.bam chr1:1000-2000 | bedtools intersect -f 1.0 -b region.bed -abam - | samtools view - > yyy.sam
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