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SEQLinkage output run in MERLIN results in "Requires impossible recombination pattern" Error #19
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I also tried using
I would like to have optimized binning into haplotypes with a separate position for each haplotype. Any suggestions on how to do that would be appreciated. |
Thanks @oleraj for the report. This issue is related to recombination events which we most recently discussed in a related project: We should make some updates this week on that issue, depending on @percylinhai 's schedule. I suppose we can try fix the genetic map distance along the line. I'll discuss with @percylinhai and make adjustments. Options --bin happens after these sub-regional markers are generated. |
Great, thanks for the reply and glad to hear you're planning some updates on this. |
@oleraj sorry we've done this a while ago but forgot to update you here. @percylinhai has implemented a fix that should give different genetic distance for subregions, based on their physical positions. Please try pulling our docker images again and test. |
Hi,
I'm running SEQLinkage on 6 families with an autosomal dominant trait we have previously mapped. I'm using this set of families to test SEQLinkage to see if we can recapitulate the results.
I have no issues running SEQLinkage:
However when I run the results in MERLIN all of the families are skipped:
The documentation for MERLIN says this
impossible recombination pattern
error is often a result of multiple markers having the same position, which is indeed the case in the SEQLinkage output. For example:It appears that some of the markers are being split into two separate bins, but the position is the same for both, which is apparently a problem for MERLIN. It seems that SEQLinkage should construct a new position for each split marker based to avoid issues with MERLIN. I'm using the default option for
--bin
, which uses LD to bin the variants. Is there any way to use this LD binning method that will produce output suitable for MERLIN, i.e., different position for each marker?Thanks!
Andrew
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