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

aehrc / TRIBES

Finding cryptic relationships to boost disease gene detection

Other

12 stars 5 forks source link

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

Open natwine opened 5 years ago

natwine commented 5 years ago

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 commented 5 years ago

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)