Need help with Plink map file

mstagliamonte · 08-31-2018, 08:50 AM

Hi,

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,
Max

vivek_ · 09-03-2018, 01:27 AM

You could set it to 0 and not have any issues as long as 1 & 4 are accurate.

mstagliamonte · 09-04-2018, 06:33 AM

Hi, Vivek,

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

Thank you,
Max

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08-31-2018, 08:50 AM	#1
mstagliamonte Member Location: Florida Join Date: Feb 2013 Posts: 33	Need help with Plink map file Hi, 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, Max

09-03-2018, 01:27 AM	#2
vivek_ 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.

09-04-2018, 06:33 AM	#3
mstagliamonte Member 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, Max