If you are interested in indels, particularly very long deletions that are common in cancer, I recommend mapping with BBMap, which outperforms everything on indel accuracy. There's also a thread for it, here:
As for what you call variations with, I'm not sure what's best. GATK and samtools pileup are commonly used. Just make sure that whatever tool you use does NOT reassemble or realign indel-containing reads, because it will probably do a worse job than BBMap's raw output.
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The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...-
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Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...-
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