Too many mendelian errors in CHP markers

[changebio]

pseudomaker cannot handle mendelian errors in CHP markers. @gaow
I tried to add '--skipmendelerrors', it didn't work.

[gaow]

@changebio how can there still be Mendelian errors in the generated markers? We did check for Mendelian error before doing the recoding and CHP should not introduce such errors. LINKAGE program check them too. We cannot skip these errors. We must understand what's going on.

[changebio]

Some thoughts to reduce recombination

1. filter common variants before phasing
2. filter variants only occurred once in a family (singleton) before phasing
3. remove families with recombination more than 3

For example in TPTEP1 gene.
49% of families has recombination less or equal to 3. After using filter 1 and 2, it increase to 82%.
In 989 family, there are 31 recombinations. Using filter 1, the recombinations reduce to 19. Using filter 1 and 2, the recombination reduce to 3.