ERROR: Map file must have the same number of loci as hap file! Map file has 0 SNPs

evotools / hapbin

Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)

GNU General Public License v3.0

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ERROR: Map file must have the same number of loci as hap file! Map file has 0 SNPs #40

Open shreyashruti opened 7 years ago

shreyashruti commented 7 years ago

Hi. I am trying to calculate EHH and IHs score from 1000 genomes data using hapbin. And the error I am getting is "Map file must have the same number of loci as hap file! Map file has 0 SNPs". Please help me fix the issue

@camaclean please look into it

Thanks in advance

camaclean commented 7 years ago

How are you making your map file? For the 1000 Genomes data, you can use tools/make_map.py to generate a .map file.

shreyashruti commented 7 years ago

@camaclean Thanks a ton for replying. Where can I get tools/make_map.py from? I couldnt find it in hapbin/tools

camaclean commented 7 years ago

Woops, it looks like it was only in my fork.

Until it's merged, see #41.

camaclean commented 7 years ago

It's merged, now. You can run it as ./make_map.py --chromosome 22, for instance.