Hello, I developed a pipeline starting with read filtering, mapping, and variant detection using Minipileup. When I execute the pipeline on my dataset, I find a certain percentage of variants at a specific position (40%); this mutation is an insertion. When a friend of mine executes his own pipeline using another algorithm (not Minipileup), he detects 75% of that same variant. I asked him to send me his BAM file so that I could apply the Minipileup algorithm directly to it; I found 42%. I'm now wondering whether my algorithm or his is more efficient.
I also tried clair3 on both my bam and also the bam generated by my friend and I found 42% and 44% respectively
Hello, I developed a pipeline starting with read filtering, mapping, and variant detection using Minipileup. When I execute the pipeline on my dataset, I find a certain percentage of variants at a specific position (40%); this mutation is an insertion. When a friend of mine executes his own pipeline using another algorithm (not Minipileup), he detects 75% of that same variant. I asked him to send me his BAM file so that I could apply the Minipileup algorithm directly to it; I found 42%. I'm now wondering whether my algorithm or his is more efficient. I also tried clair3 on both my bam and also the bam generated by my friend and I found 42% and 44% respectively