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  • 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

  • #2
    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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