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Old 11-06-2016, 02:45 AM   #1
dovah
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Location: Russia

Join Date: Jul 2014
Posts: 18
Default extended cigar in gmap

Hi all,

I am aligning pacbio reads to a reference genome using gmap. Do you know how to output an extended CIGAR in output sam file from gmap v 2016.08.10?

My command is:
Code:
gmap -d gmapDB -D path/to/gmapDB/ reads.fasta -f samse > alignment.sam
Thanks in advance
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Old 11-08-2016, 12:47 PM   #2
twu
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Location: South San Francisco, CA

Join Date: Oct 2011
Posts: 17
Default Extended CIGAR strings in GMAP

I have just added this feature in version 2016-11-07. Just add the option

--sam-cigar-extended

to gmap.

Regards,

Thomas Wu
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