Removal of alternative haplotype chromosomes for expression

[pcg]

A quick question,

Do most people exclude the contigs and haplotype chromosomes from the Human genome (hg19) from their GTF annotation files for chromosome i.e.

GL000191.1
GL000192.1
GL000193.1
GL000194.1
GL000195.1
GL000197.1
GL000199.1
GL000200.1
GL000201.1
GL000204.1
GL000205.1
GL000209.1
GL000211.1
GL000212.1
GL000213.1
GL000214.1
GL000216.1
GL000218.1
GL000219.1
GL000220.1
GL000221.1
GL000222.1
GL000223.1
GL000224.1
GL000225.1
GL000227.1
GL000228.1
GL000229.1
GL000230.1
GL000233.1
GL000236.1
GL000237.1
GL000238.1
GL000239.1
GL000240.1
GL000241.1
GL000242.1
GL000243.1
GL000247.1
HSCHR17_1
HSCHR6_MHC_APD
HSCHR6_MHC_COX
HSCHR6_MHC_DBB
HSCHR6_MHC_MANN
HSCHR6_MHC_MCF
HSCHR6_MHC_QBL
HSCHR6_MHC_SSTO

If so why particularly if you are only interested in expression of genes? And why does the pre-built index for bowtie not contain contigs unplaced or unlocalized sequences and alternate haplotype

[dtc]

do you have any idea of this , i have the same problem,thank you

[cgjkjk]

A haplotype is a group of genes within an organism that was inherited together from a single parent. The word "haplotype" is derived from the word "haploid," which describes cells with only one set of chromosomes, and from the word "genotype," which refers to the genetic makeup of an organism. A haplotype can describe a pair of genes inherited together from one parent on one chromosome, or it can describe all of the genes on a chromosome that were inherited together from a single parent. This group of genes was inherited together because of genetic linkage, or the phenomenon by which genes that are close to each other on the same chromosome are often inherited together. In addition, the term "haplotype" can also refer to the inheritance of a cluster of single nucleotide polymorphisms (SNPs), which are variations at single positions in the DNA sequence among individuals.

By examining haplotypes, scientists can identify patterns of genetic variation that are associated with health and disease states. For instance, if a haplotype is associated with a certain disease, then scientists can examine stretches of DNA near the SNP cluster to try to identify the gene or genes responsible for causing the disease.

reference:http://www.nature.com/scitable/defin...haplotypes-142