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Old 08-31-2018, 08:50 AM   #1
Location: Florida

Join Date: Feb 2013
Posts: 33
Default Need help with Plink map file


I plan to phase my non-human organism genomic data using Shapeit2. I have recombination data available from literature, but I am struggling to understand how to set up the map file. I have read around but still not sure how to build the file. This is the description of the map file:

This file can be SPACE or TAB delimited. Each line corresponds to a SNP. The 4 columns are:
1) Chromosome number [integer]
2) SNP ID [string]
3) SNP genetic position (cM) [float]
4) SNP physical position (bp) [integer]

I am not sure on the interpretation of column 3. Let's say I have a known recombination rate of 13mbp/cM and 4 SNPs in position 500, 10,000, 20,000, 33,000 on chromosome 2 : how should the map file look like?

Thank you for your kind attention,
mstagliamonte is offline   Reply With Quote
Old 09-03-2018, 01:27 AM   #2
PhD Student
Location: Denmark

Join Date: Jul 2012
Posts: 164

You could set it to 0 and not have any issues as long as 1 & 4 are accurate.
vivek_ is offline   Reply With Quote
Old 09-04-2018, 06:33 AM   #3
Location: Florida

Join Date: Feb 2013
Posts: 33

Hi, Vivek,

Thank you for your answer. Can you elaborate on that a bit, please?

Thank you,
mstagliamonte is offline   Reply With Quote

map file, phaseit, phasing, plink, recombination rate

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