How to perform relatedness across multiple trio cohort ?
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4 months ago
dare_devil ★ 1.4k

I have 15 trio cohort and I have generated the combined vcf file across all the trio cohort using GATK Best Practice

My trio data look as folows:

FamID   IndID   PatID   MatID   Sex     Phenotype
1       in1     Pat1    Mat1    1       2
1       Pat1    0       0       1       0
1       Mat1    0       0       2       0
2       in2     Pat2    Mat2    1       2
2       Pat2    0       0       1       0
2       Mat2    0       0       2       0
..       ..          ..        ..      ..        ..
15      in15    Pat15   Mat15   1       2
15      Pat15   0       0       1       0
15      Mat15   0       0       2       0

Now I wanted to check relatedness among the each trio set (son, father, mother). I used vcftools to check the relatedness as follows:

vcftools --gzvcf cohort.g.vcf.gz --relatedness

I got strage results as follows:

INDV1   INDV2   RELATEDNESS_AJK
001C1   001C1   -nan
001C1   001P1   -nan
001C1   001P2   -nan
001C1   001c2   -nan
001C1   003C    -nan
001C1   003P1   -nan
001C1   003P2   -nan
001C1   004C    -nan
001C1   004P1   -nan
001C1   004P2   -nan

What am I doing wrong?

trio vcftools relatedness • 171 views
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