Question: Sex inconsistency in 1000 genomes phase 3 TSI samples
0
gravatar for Apprentice
15 days ago by
Apprentice20
Apprentice20 wrote:

Hi.

I'm going to check sex consistency using 1000 genomes phase 3 TSI samples. As a result, inconsistency in sex was detected in 3 samples. The IDs were NA20506, NA20530, and NA20533. So, I would like to know that this inconsistency was often know? Should I removed the samples in chrX SNP analysis?

To check the sex, I did following process.

I got a vcf file of chrX from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/. The file name was ALL.chrX.phase3_shapeit2_mvncall_integrated_v1b.20130502.genotypes.vcf.gz.

First, the file was converted to bed file format using PLINK 1.9. Second, SNPs in the file were splited into chrX SNPs and chrXY SNPs using plink --split-x. Third, EUR samples were extracted from the file using plink --keep. Next, SNPs with MAF<0.01, HWE P < 1e-6, or CR<0.98 were excluded. Finally, I checked sex based on the file using PLINK --check-sex.

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ADD COMMENTlink modified 14 days ago by chrchang5235.0k • written 15 days ago by Apprentice20
2
gravatar for chrchang523
14 days ago by
chrchang5235.0k
United States
chrchang5235.0k wrote:

No. You need to reselect your --check-sex thresholds based on the data. As long as there is a clean separation between females and males, you're fine; it's fine if some female F values are much higher than the default 0.2 lower threshold.

(The 0.2 and 0.8 default thresholds will be eliminated in the future; they're only present at all in PLINK 1.9 to preserve backward compatibility.)

ADD COMMENTlink written 14 days ago by chrchang5235.0k
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