AncestryMap is a software package that allows finding skews in ancestry that are potentially associated with disease genes in recently mixed populations.

References:

• N.Patterson, N.Hattangadi, B.Lane, K.E.Lohmueller, D.A.Hafler, J.R.Oksenberg, S.L.Hauser, M.W.Smith, S.J.O’Brien, D.Altshuler, M.J.Daly, and D.Reich
  Methods for High-Density Admixture Mapping of Disease Genes
  Am. J. Hum. Genet. 74:979-1000, 2004.

• AncestryMap Tutorial.
• AncestryMap Software Documentation.

• Module Name: AncestryMap (see the modules page for more information)
• Unusual environment variables set
  • AMAP_BIN       executable directory
  • AMAP_SRC       source code directory
  • AMAP_DATA    sample data directory

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load AncestryMap
[+] Loading AncestryMap 6210 ...

[user@cn3144 examples]$ cp $AMT_DATA/* .

[user@cn3144 examples]$ ancestrymap -p param0
parameter file: param0
output: (null)
### THE INPUT PARAMETERS
PARAMETER NAME: VALUE
risk: 1.5
indivname: indiv.dat
snpname: snpcnts
genotypename: geno.dat
tlreest: YES
seed: 1011
splittau: YES
fancyxtheta: YES
checkit: YES
details: YES
numburn: 0
numiters: 0
emiter: 10
dotoysim: NO
cleaninit: YES
reestiter: 5
indoutfilename: indjunk
snpoutfilename: snpjunk
## ANCESTRYMAP version: 6210

###GENETIC DISTANCE FOR ALL CHROMOSOMES
##Chr_Num: chromosome num, First_SNP and Last_SNP: First and last markers, Gen_dist: Genetic distance
         Chr_Num    First_SNP     Last_SNP           Gen_dist
chrom:     1  first:     0  last:  478 distance:     2.834
chrom:     2  first:   479  last:  910 distance:     2.647
chrom:     3  first:   911  last:  1276 distance:     2.227
...
chrom:    20  first:  5330  last:  5492 distance:     1.067
chrom:    21  first:  5493  last:  5586 distance:     0.604
chrom:    22  first:  5587  last:  5699 distance:     0.711
chrom:    23  first:  5700  last:  5902 distance:     1.180
total distance:    36.242
calling setstatus

emiter: 10
reestiter: 5
trashdir: /var/tmp
###HETXCHECK RESULTS BEGIN
##                      SNP_ID  NUM_HET NUM_HOMOZY
hetxcheck            rs6530109      0      600
hetxcheck            rs2128516      0      600
...
hetxcheck           rs10127175      0      600
hetxcheck            rs5945413      0        0
hetxcheck             rs884840      0      600

###COUNTS
Num of fake Markers: 3622  Num of real Markers: 2281 Spacing between fake markers:     0.010
Num of Markers: 5903   Num of Samples:  1201
Num of Cases:  601 Num of Controls:  600   Num of Ignored Samples: 0
dup? toyindiv:539 toyindiv:1200
 match: 2260 mismatch: 0   2260 2260
dup.  toyindiv:539 ignored

### CHECKGENO RESULTS FOLLOW:
Num good genotypes: 2714260  Num bad genotypes:  0

###PHYSCHECK RESULTS FOLLOW:
##        SNP1_ID        SNP2_ID   SNP1_GEN_POS   SNP2_GEN_POS  SNP1_PHYS_POS  SNP2_PHYS_POS
###HWCHECK RESULTS FOLLOW:
##                   SNP_ID  SNP_INDEX    CHR_NUM   HW_SCORE
hwcheck             rs819980     0        1       -1.595
hwcheck           rs10907185     1        1        0.376
hwcheck             rs897634     4        1       -1.861
...
hwcheck            rs4824056  5694       22       -2.308
hwcheck             rs138823  5695       22       -2.112
hwcheck            rs6520141  5696       22       -1.517
hwcheck            rs8142477  5698       22       -2.327
hwcheck             rs140514  5699       22       -0.021

hwstats (chrom  1) ave:    -1.110 sigma:   -15.543
hwstats (chrom  2) ave:    -1.330 sigma:   -17.183
hwstats (chrom  3) ave:    -1.278 sigma:   -15.286
hwstats (chrom  4) ave:    -1.003 sigma:   -11.304
hwstats (chrom  5) ave:    -1.322 sigma:   -15.698
hwstats (chrom  6) ave:    -1.071 sigma:   -11.536
hwstats (chrom  7) ave:    -1.088 sigma:   -12.016
hwstats (chrom  8) ave:    -1.157 sigma:   -12.247
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. AncestryMap.sh). For example:

#!/bin/bash
# this file is called admix.sh

module load AncestryMap

cp $AMT_DATA/* .

ancestrymap -p param0 > data0.out
ancestrymap -p param1 > data1.out
ancestrymap -p param2 > data2.out

Submit this job using the Slurm sbatch command.

sbatch  [--mem=#] AncestryMap.sh

Create a swarmfile (e.g. AncestryMap.swarm). For example:

cp $AMT_DATA/* .
ancestrymap -p param0 > data0.out
ancestrymap -p param1 > data1.out
ancestrymap -p param2 > data2.out

Submit this job using the swarm command.

swarm -f AncestryMap.swarm [-g #] --module AncestryMap