How to read Cigar Strings in SAM file

The ‘CIGAR’ (Compact Idiosyncratic Gapped Alignment Report) string is how the SAM/BAM format represents spliced alignments. Understanding the CIGAR string will help you understand how your query sequence aligns to the reference genome.
in this video, I hope to you through with you the basic format for the CIGAR strings with a few example. hopefully that would help anyone struggling to understand this format
Email: liquidbrain.r@gmail.com
Github: github.com/brandonyph
Twitter: / brandon_yeoph

Пікірлер: 7

  • @user-cg9iq2hp6j
    @user-cg9iq2hp6j2 ай бұрын

    thanks! really helpful!

  • @taehoonkim7819
    @taehoonkim78193 ай бұрын

    Also note that M means either match or mismatch, so that it is compatible with the alignment.

  • @subodhgaikwad3366
    @subodhgaikwad33662 жыл бұрын

    Thanks !

  • @irfanalahi380
    @irfanalahi3803 жыл бұрын

    Very helpful. Is there any tool where if I provide a genomic position and a read from a bamfile it will output the corresponding base from the read (not from reference sequence) by parsing the CIGAR string?

  • @user-ef7ih9ww4g

    @user-ef7ih9ww4g

    Жыл бұрын

    Hello, I found it fanxingguo.blogspot.com/2022/08/test.html

  • @Sun48100
    @Sun481003 жыл бұрын

    This is helpful but what about character H and X?

  • @LiquidBrain

    @LiquidBrain

    3 жыл бұрын

    You can get a detail explanation of the string here: www.drive5.com/usearch/manual/cigar.html