Counting Specific Genetic Variants in IGV Using Fixed Read Data

Question

[safeassli]

Is there a way to count the number of times a specific variant appears in IGV? I have a fixed number of reads (10,000), and I want to count how many times I encounter this specific variant. I want to count the occurence of the insertions of 6 bases. NB: I want to validate my pipeline where I use a tool to count the occurrence of the variant (pileup).

[Pierre Lindenbaum]

how about 'just' calling the variants as a VCF file ? you'll get the information in the FORMAT/AD field.

[safeassli]

thank you , Yes, I know that it would be in the FORMAT/AD field, but I'm looking for another method to compare my results. In fact, I can't find the same results as my colleague. It’s true that we are not using the same algorithm, but when I use his BAM file with my algorithm, I generate the same results as my results. For this reason, I want to verify the findings using IGV or an equivalent tool. the idea is to compare the 2 algorithm (Does my algorithm miscalculate these insertions or not)

[GenoMax]

but I'm looking for another method to compare my results

How would another method change the counts of the specific insertion from the same BAM file?

Have you looked at igvtools as an option.

[safeassli]

I don't know since we don"t get the same percentage of variation , we said maybe the problem is related to the fact that we use different variant calling algorithms , that's why I'm looking for another method