NCHROBS

[Sander W. van der Laan MSc.]

Hi,

I noticed a little thing. I merged the EUR populations from 1000G into one file - yeah call me crazy. Anyway, there are 379 individuals in these files combined. When I run the --freq flag it produces a correct file, except for one thing. The NCHROBS is equal to 379. Shouldn’t that be 758, i.e. the count of the number of alleles per SNP: 2x sample size?

Below the log of the merge, the frequency check and a head of the freq-file.

Thanks!

Sander

PLINK v1.90b3a 64-bit (12 Jan 2015)

7 arguments: --bfile 1000Gp1v3.20101123.CEU --make-bed --merge-list eur_merge.txt --out 1000Gp1v3.20101123.EUR

Hostname: Sanders-MacBook-Pro.local

Working directory: /Users/sanderwvanderlaan/PLINK/references/1000G/Phase1/PLINK

Start time: Mon Jan 26 10:37:00 2015

Random number seed: 1422265020

16384 MB RAM detected; reserving 8192 MB for main workspace.

Performing single-pass merge (379 people, 38248779 variants).

Merged fileset written to 1000Gp1v3.20101123.EUR-merge.bed +

1000Gp1v3.20101123.EUR-merge.bim + 1000Gp1v3.20101123.EUR-merge.fam .

38248779 variants loaded from .bim file.

379 people (178 males, 201 females) loaded from .fam.

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 379 founders and 0 nonfounders present.

Calculating allele frequencies... done.

Warning: 687266 het. haploid genotypes present (see 1000Gp1v3.20101123.EUR.hh

).

Total genotyping rate is 0.999953.

38248779 variants and 379 people pass filters and QC.

Note: No phenotypes present.

--make-bed to 1000Gp1v3.20101123.EUR.bed + 1000Gp1v3.20101123.EUR.bim +

1000Gp1v3.20101123.EUR.fam ... done.

End time: Mon Jan 26 11:19:46 2015

PLINK v1.90b3a 64-bit (12 Jan 2015)

5 arguments: --bfile 1000Gp1v3.20101123.EUR --freq --out 1000Gp1v3.20101123.EUR.FREQ

Hostname: Sanders-MacBook-Pro.local

Working directory: /Users/sanderwvanderlaan/SNP_suites/MANTEL/RESOURCES/1000Gp1v3_EUR

Start time: Mon Jan 26 11:57:59 2015

Random number seed: 1422269879

16384 MB RAM detected; reserving 8192 MB for main workspace.

38248779 variants loaded from .bim file.

379 people (178 males, 201 females) loaded from .fam.

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 379 founders and 0 nonfounders present.

Calculating allele frequencies... done.

Warning: 687266 het. haploid genotypes present (see

1000Gp1v3.20101123.EUR.FREQ.hh ).

Total genotyping rate is 0.999953.

--freq: Allele frequencies (founders only) written to

1000Gp1v3.20101123.EUR.FREQ.frq .

End time: Mon Jan 26 11:59:47 2015

CHR SNP A1 A2 MAF NCHROBS

1 chr1:10583 G A 0.2071 379

1 chr1:10611 C G 0.0211 379

1 chr1:13302 C T 0.1372 379

1 chr1:13327 G C 0.0396 379

[Christopher Chang]

Hmm, yes, that should be 758.  Could you create a fileset with just the first 10 variants, verify that the bug still manifests, and then send it to me so I can investigate this?

[Christopher Chang]

(I failed to reproduce this with my own 1000g all-chromosomes file.)