6.2.3 Output Details
Next we will discuss the output in detail to the standard output, in the case where details = YES, checkit = YES, numburn = 0 and numiters= 0. As always this output can be redirected to a file for easier viewing.
- Input parameter file name
- Values of all the parameters specified in this file
- Genetic distance for all chromosomes:
- Total genomic distance
Here is an example of the output generated:
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: 4 first: 1277 last: 1617 distance: 2.131
chrom: 5 first: 1618 last: 1961 distance: 2.012
chrom: 6 first: 1962 last: 2272 distance: 1.914
chrom: 7 first: 2273 last: 2581 distance: 1.871
chrom: 8 first: 2582 last: 2862 distance: 1.677
chrom: 9 first: 2863 last: 3133 distance: 1.777
chrom: 10 first: 3134 last: 3420 distance: 1.809
chrom: 11 first: 3421 last: 3682 distance: 1.552
chrom: 12 first: 3683 last: 3961 distance: 1.723
chrom: 13 first: 3962 last: 4169 distance: 1.258
chrom: 14 first: 4170 last: 4360 distance: 1.162
chrom: 15 first: 4361 last: 4559 distance: 1.245
chrom: 16 first: 4560 last: 4772 distance: 1.340
chrom: 17 first: 4773 last: 4971 distance: 1.272
chrom: 18 first: 4972 last: 5161 distance: 1.160
chrom: 19 first: 5162 last: 5329 distance: 1.069
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
- Count of individuals, cases, controls and ignores used in the analysis; and also the number of real and fake markers
- Fastdup results
- Checkgeno results
- Physcheck results
###HETXCHECK RESULTS BEGIN
## SNP_ID NUM_HET NUM_HOMOZY
hetxcheck rs6530109 0 600
hetxcheck rs2128516 0 600
hetxcheck rs16984097 0 0
hetxcheck rs5948775 0 600
hetxcheck rs7884299 0 600
hetxcheck rs5978365 0 600
hetxcheck rs1474458 0 600
hetxcheck rs1013549 0 600
hetxcheck rs1007420 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
- Hardy-Weinberg results
- Checkdup results
###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 rs2817159 6 1 -0.582
hwcheck rs1181868 9 1 0.134
hwcheck rs7548756 12 1 -0.058
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 (autosomes) ave: -1.210 sigma: -56.448
###CHECKDUP RESULTS FOLLOW:
##Indiv_Id1 Indiv_Id2
##Num of genotypes matched: Num of genotypes mismatched
##If the status of the two individuals does not match Status1: Status2
match prob. mean: 0.464 s.dev: 0.058
## no iterations: end of run