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  • Looking for tools for calling snv and indel(Somatic Variant)

    Dear expert,
    I am working on exome-seq data.
    Looking for tools for calling snv and indel(Somatic Variant) in matched tumor-normal samples. Any suggestions?
    Thank you very much in advance.

  • #2
    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:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    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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