GATK VariantsToBinaryPed and PLINK

[gibberwocky]

Hopefully someone can point out what I'm doing wrong.

I have called variants for 4 chickens separately in GATK using the Haplotype caller, and the VCF files have later been combined using the CombineVariants tool. The resulting VCF file has then been converted to PED format using the VariantsToBinaryPed tool. No errors were generated at any point.

However, when using the binary file set in plink there appears to be an issue. For instance, when calculating allele frequency for 77k SNPs the MAF is NA for all SNPs, as the NCHROBS is 0 for all SNPs, e.g.

 CHR              SNP   A1   A2          MAF  NCHROBS
  24      Var-24-1055    A    T           NA        0
  24      Var-24-1137    T    A           NA        0
  24      Var-24-1263    G    A           NA        0

Looking at the VCF file that was fed into the VariantsToBinaryPed tool indicates that these SNPs are present and genotyped, e.g.

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HA1A22AHB1A16A	JA1A17A	JB1A25B
24	1055	.	T	A	484.77	PASS	AC=8;AF=1.00;AN=8;DP=129;FS=0.000;MLEAC=2;MLEAF=1.00;MQ0=0;set=Intersection	GT:AD:DP:GQ:PL	1/1:0,26:26:54:513,54,0	1/1:0,38:38:99:1138,117,0	1/1:0,35:35:99:977,108,0	1/1:0,30:30:93:890,93,0
24	1137	.	A	T	181.77	PASS	AC=2;AF=0.500;AN=4;DP=65;MLEAC=1;MLEAF=0.500;MQ0=0;set=HA1A22A-JB1A25B	GT:AD:DP:GQ:PL	0/1:16,10:26:99:210,0,208	./.	./.	0/1:19,20:39:99:372,0,261
24	1263	.	A	G	170.77	PASS	AC=2;AF=0.500;AN=4;DP=38;MLEAC=1;MLEAF=0.500;MQ0=0;set=HA1A22A-JB1A25B	GT:AD:DP:GQ:PL	0/1:14,10:24:99:199,0,172	./.	./.	0/1:6,8:14:89:122,0,89

Can anyone advise?

Cheers

D

[chrchang]

PLINK assumes chromosome 24 is the Y chromosome, and forces all nonmale Y chromosome genotypes to missing.

With PLINK 1.07, you can hack your way around this by using --dog to force the correct chromosome count. PLINK 1.9 has the more general --chr-set flag for this (and it can also directly import VCF files with --vcf).

[gibberwocky]

Much obliged, that solved the problem, figured it would be something trivial.

D