extended cigar in gmap

[dovah]

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:

gmap -d gmapDB -D path/to/gmapDB/ reads.fasta -f samse > alignment.sam

Thanks in advance

[twu]

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