Section 11

14. Description of the auxiliary package cntmono

In this section we will discuss the auxiliary software cntmono included with ANCESTRYMAP. This program takes as input, files with genotype data, and corresponding individual and marker data for the modern counterparts of the ancestral parental population subgroups and creates an output file which has the counts for the reference and variant alleles for these populations. This can in turn be used by the ancestrymap program as its input marker/ snp file. For a short tutorial on how to run this program click here.

How to run the program

The command line arguments for cntmono are p (parameter file) which is mandatory, V (version number) and v (verbose mode), same as for ancestrymap. To run this type on the commandline:

>> cntmono –p parcmono or ./cntmono –p parcmono

Use the file parmono in the examples/ directory as a sample file to create parcmono. This file has names for the following files:

§         Genotype Data: String: genotypename

SNP_ID

INDIV_ID

Vart_allele_cnt

rs112

I1

1

rs113

I2

0

rs114

I3

2

§         Marker Data: String: snpname

SNP_ID

Chr_Num

Gen_Pos

Phys_Pos

rs112

1

0.3455676

114556

rs113

2

0.566879

1400898

§         Individual Data: String: indivname

INDIV_ID

Gender

Status

I1

F

CEPH

I2

M

BOTSWANA

I3

M

GHANA

The value in the Status field is that of the ethnicity of the sample. This can be as varied as the examples shown above, or as narrow as AFRICAN, EUROPEAN, ASIAN, etc.

§         Population A subgroup data: String: aglistname

This contains a list of ethnicities that are classified as population A subtype

Ethnicity

Beni

Botswana

§         Population B subgroup data: String: eglistname

This contains a list of ethnicities that are classified as population B subtype

Ethnicity

CEPH

Italy

§ Output Data: String: output

The output file has the following columns

  • SNP_ID
  • Chromosome number
  • Genetic position
  • Physical position
  • Population A reference allele count
  • Population A variant allele count
  • Population B reference allele count
  • Population B variant allele count
  • Number of valid genotypes