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extended output columns

Hi, I use the option to get extended output from mutect and it works well. Unfortunately I cannot find a detailed description of all the columns, only the ones that are in the regular output. Is it possible to have this kind of documentation?
thanks a lot

Answers

  • yl3yl3 Member

    I'm interested in this as well since extended output seems to be providing a lot of useful information w.r.t. filtering the false positives. Could we have a brief description of the extended output columns? Thanks

  • danielvodanielvo Member

    Hello,

    I would also wish to ask for description of the extended_output-only columns. I am attaching a file which lists all the columns together with their number. Description is included for all the columns for which it was already provided at http://www.broadinstitute.org/cancer/cga/mutect_run.

    I have also noticed that columns 54-57 sometimes have value "n/a", while columns 58-60 sometimes have their values missing (rather than having "n/a" values as well). In column 68, nearly all failure reason labels have underscores replacing spaces between individual words, but "DBSNP Site" is an exception. These inconsistencies could be inconvenient while parsing the output. Perhaps they are of interest with respect to a future release? (I am using muTector v1.0.47986.)

    Best regards,
    Daniel

  • umarumar Member

    Hi,
    I was wondering if some can tell me how to use the extended output option. I am using ## muTector v1.0.47986 as well. Another question is that if I use the -vcf option can I still get the extended column output as well. I have used couple of other mutation callers in past and mutect has given me the lowest false positive so far.
    Thanks,
    Umar

  • danielvodanielvo Member

    Hi there.

    You can use the "--enable_extended_output" command line option. I am not sure about the VCF's content in that case, but you can always run MuTect on a small genomic interval to do a quick test.

  • umarumar Member

    Thanks. I used both the extended output option and the vcf and got the expected output. It is very helpful to know why a mutation site was keep or rejected. It will be nice to know what all the headers in this table actually mean.

  • ltononltonon Member

    I would really need an explanation about the extended output columns. Especially about the biais and filters.
    Does someone managed to have one?

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