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

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

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

• 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