indelocator

Hi
I have been trying to get my hands on help docs or command line examples for the indelocator ...
It does not seem to have any support yet still part of the tool for cancer sample analysis.
Do you have any recommendations? If it is not recommended then why make it public?

Many of us would like to understand how to run it, we can probably do our own filtering on verbose output.

Thanks,
Barak

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  • barakbarak Member

    OK. thanks a lot.
    Looking fw for a new indel caller :)
    Barak

  • VewehrVewehr Czech RepublicMember

    So what is the best tool for somatic indel detecting available now? I am a newbie in this area of expertise and I am searching for some tool to call somatic indels in our set of data. Thank you.

  • dklevebringdklevebring Member

    My two cents: I use IndelLocator (the one which is available) and pindel and filter results using Fisher's exact test, with a hard cutoff of the normal allele fraction.

    @kcibul Any timeline for when the successor might become available? Are we talking month(s) or year(s)? A very very rough estimate would be great. Even a beta version I think would benefit many in the community. Thanks.

  • barakbarak Member

    I use a Shimmer at the moment. Roughly the same approach using samtools.

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