I am new to exome sequencing analysis. I have been looking into the theory and tried using galaxy for the same. I got 2 mutations following a published pipeline from the shared data (which uses freebayes) but only one of them was confirmed by Sanger Sequencing.
Looking back at my SNP-Sift output, I see that although the unconfirmed variant is of good quality [“QUAL” is good], the CIGAR string for that variant is just represented as “CIGAR=1X”.
From a theoretical point of view, what I could understand is that , CIGAR strings is generally represented as some matches, then some mismatches/insertion/deletion and then some matches. So, I am unable to understand how it can just be “CIGAR=1X”. If it is possible, please tell what does it say about the quality of that variant.
Any help would be appreciated.