Query regarding haplotypes e.g. chr6_dbb_hap3

[doraemon]

Hi,

I've been doing some analysis of exons/introns based on the hg19 assembly and RefSeq annotation track from UCSC.

A number of chromosomes represent haplotype alleles or unplaced contigs.

If doing analysis of exons/introns ... (e.g. avg size of introns across chr6 / chr7 as an example) - should one exclude these?

chr19
chr19_gl000209_random
chr1_gl000191_random
...
chr4
chr4_ctg9_hap1
chr5
chr6
chr6_apd_hap1
chr6_cox_hap2
...

Thanks for any advice.