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add genetic length (cM) of segments to final .match file #3

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natwine opened this issue Oct 8, 2019 · 1 comment
Open

add genetic length (cM) of segments to final .match file #3

natwine opened this issue Oct 8, 2019 · 1 comment
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@natwine
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natwine commented Oct 8, 2019

please could you add genetic length in cM to the final post-masked .match files. Ideally these will be all the segments that have been used in the relationship estimation step.

We agreed to adjust GERMLINE analysis step to identify segments 3cM or larger. Segment length will be set as a parameter for the user to specify, with the default value being 3cM.
@piotrszul
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Made the following modifications:

  • added a config parameter min_seg_len (default = 3.0 [cM]) which is being used for germline and IBD0 estimation. It can be set either in config.yaml or from command line with --config min_seg_len=2.0 etc.
  • ersa masking step (FPI) now outputs segments with length in [cM].
  • the IDB0/relatedness estimation now (IBD) now outputs an extra file XXX_IBD-segments.match.gz with the segment that were used for IBD0/degree estimation (in germline match file format)

@piotrszul piotrszul mentioned this issue Oct 10, 2019
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piotrszul added a commit that referenced this issue Oct 10, 2019
@piotrszul
[#3] add genetic length (cM) of segments to final .match file (#4)
e46178b 
* Added saving of actual segments used for IBD estimation in germline format to IBD estimation step

* Ouput from masking not produced segment with genetic lenght in cM

* Added "min_seg_len" parameter to use for germline and estimation:"
@piotrszul piotrszul assigned piotrszul and natwine and unassigned piotrszul Oct 10, 2019
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