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Old 03-16-2010, 06:54 AM   #1
jdiezperezj
Junior Member
 
Location: spain

Join Date: Mar 2010
Posts: 3
Default Sam 2 ace

Hi everyone,
This is my first post on the list. I would like to know if there is a tool/script ... to convert from SAM format to ACE format.
Cheers.
Javi
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Old 05-24-2012, 07:10 AM   #2
nataliaTS
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Location: Barcelona, Spain

Join Date: Feb 2012
Posts: 1
Default SAM/BAM to ...

Hi!!!
I have the same problem. Anyone know how to covert SAM/Bam to other format like ACE???

thanks
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Old 05-24-2012, 01:08 PM   #3
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

At least for ACE,

- convert SAM to BAM using samtools

- use consed for the bam to ace conversion,

Docs say (v22 or greater),
"-Create an ace file from a bam file: consed -bam2Ace
You can make an ace file out of just a targeted region of the
reference sequence or out of the entire reference sequence.
Cigars are shown in consed. By default, shallowerDepth
(below) is included.
"

hth, Sven
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