Extracting alternate loci from fasta genome

[Jane M]

Dear all,

I downloaded full reference fasta genomes for hg19, mm9 and mm10 from gencode. They include reference chromosomes, scaffolds, assembly patches and haplotypes.
For a specific purpose, I want to remove haplotypes.
I did not manage to find a description of the nomenclature used for the contigs in fasta file.
In the hg19 reference genome I use, there are 297 contigs. One can see for example:

>chr1 1
>chr2 2
...
>chrM MT
>GL877870.2 HG1007_PATCH
>GL877872.1 HG1032_PATCH
...
>GL383545.1 HSCHR10_1_CTG2 <- is it an "unlocalized sequence" ?
>GL383546.1 HSCHR10_1_CTG5
...
>GL000191.1 GL000191.1
>hg19GL000192.1 GL000192.1

I would like to know how many of them are haplotypes and which ones are they.
Is there a way to get this information?

Thank you in advance for your help.

[Jane M]

If it can help someone in the future, we can get this type of information on NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/g...ate_mammalian/
In *_report.txt files, for each contigs, there is assembled-molecule / unlocalized-scaffold / unplaced-scaffold / novel-patch / fix-patch or alt-scaffold.