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Update documentation #406

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fnothaft opened this Issue Oct 7, 2014 · 3 comments

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fnothaft commented Oct 7, 2014

What needs to be documented:

  • Coordinate systems
  • Transformation algorithms (BQSR, indel realignment, mark dups)
  • Schemas vs. models
  • Update getting started docs
  • Write variant discussion up
  • Join algorithms - how/what/why?

@fnothaft fnothaft added the enhancement label Oct 7, 2014

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antonkulaga Nov 19, 2014

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One or two tutorials with common use-cases (gene expressions, variant calling) will be extremely useful for newcomers like me ( opened an issue on that #491 )

P.S. Some people choose Adam not because of its super-format or very advanced algorithms, but because they are tired of console tools and want to use reasonable (in other words: not R and not Perl) language for dealing with common genomics tasks like gene expression analyses or variant calling together with mapreduce capabilities (to use at least several machines) and adam looks like the only lib that supports for Scala/Spark (I do not count SparkSeq because I am afraid it is abandoned)

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antonkulaga commented Nov 19, 2014

One or two tutorials with common use-cases (gene expressions, variant calling) will be extremely useful for newcomers like me ( opened an issue on that #491 )

P.S. Some people choose Adam not because of its super-format or very advanced algorithms, but because they are tired of console tools and want to use reasonable (in other words: not R and not Perl) language for dealing with common genomics tasks like gene expression analyses or variant calling together with mapreduce capabilities (to use at least several machines) and adam looks like the only lib that supports for Scala/Spark (I do not count SparkSeq because I am afraid it is abandoned)

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tdanford Nov 20, 2014

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I'll move the coordinate system page, and the FAQ, into the discussion docs today.

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tdanford commented Nov 20, 2014

I'll move the coordinate system page, and the FAQ, into the discussion docs today.

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fnothaft Jul 20, 2016

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Closing in favor of #890, #886, #878, #879, #821, #497.

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fnothaft commented Jul 20, 2016

Closing in favor of #890, #886, #878, #879, #821, #497.

@fnothaft fnothaft closed this Jul 20, 2016

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