README.md

TrioGenetics

Motivation

how to estimate all spectrum of heterozygosity between maternal and paternal haplotypes

sex chromosomes should be studied separately

what kinds of variants should be considered?

calculation method

best practises to detect different kinds of variants

Alignment

I recommend to use 'nucmer' to conduct alignment between maternal and paternal haplotypes, which is an appropriate tools to deal with highly similar sequences especially homo

SNV

show-snps -rlTHC test.delta >test1.snp

• show-snps -rlTHC test.1delta >test2.snp

Small indel

Large indel

rearrangement, inversion, translocation, inverted translocation

duplication, copy number variants

issues way to solve

• how to classify and define the variations clearly when they get overlapped?

• how to calculate the overall heterozygosity, how to deal with snp/indels within big SVs?

• how to define the CNV, unit length? how divergent between copies, local (tandem) or remote?

• the large indels which locate at the end of chromosome are caused by unplaced sequence?

• choose the best program and pratices