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I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot.
In my case I have some Illumina short data edited with Crisp-Cas9 and I want to calculate for a specific position all the frequency of the 4 nucleotides. I would like to understand if the supplementary reads aligned in that position must be taken into consideration.
I've used pysamstats to calculate and it consider them, but my doubt is more if it right to consider them, if it is normally done or not. We are doing it on human and we expect only a change of a single nucleotide variant in the region if the editing works.
I'm interested in what is done generally, if there is a "rule" to consider or not the supplementary alignment when the AF is calculated. In my case I have some Illumina short data edited with Crisp-Cas9 and I want to calculate for a specific position all the frequency of the 4 nucleotides. I was trying to understand if the supplementary reads aligned in that position must be taken into consideration.
GATK HaplotypeCaller and Mutect2 take them into consideration? I'm not looking for a specific variant caller, but if I want to take one variant caller as "reference", I would probably look at them.
Thanks a lot.