How to read Cigar Strings in SAM file
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- Опубліковано 27 сер 2024
- 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
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Also note that M means either match or mismatch, so that it is compatible with the alignment.
thanks! really helpful!
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?
Hello, I found it fanxingguo.blogspot.com/2022/08/test.html
Thanks !
This is helpful but what about character H and X?
You can get a detail explanation of the string here:
www.drive5.com/usearch/manual/cigar.html