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.
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 |
|
I3 |
M |
|
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 |
|
§ Population B subgroup data: String: eglistname
This contains a list of ethnicities that are classified as population B subtype
Ethnicity |
CEPH |
|
§ 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