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Old 07-29-2011, 05:44 AM   #1
papori
Senior Member
 
Location: berd

Join Date: Dec 2010
Posts: 179
Default merging 2 sam files

Hi all,
i was using BWA 0.5.9
i was doing samse.
i did samse for pair ends separately.
first for first pair , next to the second pair.
So , i am having now 2 files
*_1.sam
*_2.sam

Can i merge it with samtools?
If i will merge it with samtools , will the result be the same as i was doing sampe?
I am not using sampe , because i have segmentation fault with sampe, but not with sampe.

Thanks , Papori
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