Arlequin problem (different loci number among different genotypes)

Question

[wangh920]

Hello everyone,

I used PGDSpider converting my vcf to xxx.arp (Arlequin format), but the problem is that when I ran Arlequin, the following error happened:

Reading Project: 
Reading input file ...
    Reading Samples section ...
    Reading Pop_1 ... 
    Number of loci for genotype "Vernal-7" is different (26640) from that previously defined (26638) on line 17

In summary, it looks like that the number of loci is different among genotypes. But the PGDspider transferred all SNPs from VCF to this format for all genotypes, I checked the data (xxx.arp), which is correct. Also I saw the manual, they fixed this bug, look like not.

Anyone can help would be appreciated.

Hu

[lieven.sterck]

Hello wangh920,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

Answer 1

[wangh920]

I solved this problem already

[lieven.sterck]

great to hear.

if you would care to add some explanations on how or what you did to fix it , I would upvote it

[wangh920]

For sure,

The reason why this happen is because SNP calling generate a couple of biallelic SNP, such as GC, GT or GCT, GCG. These allelic will generate inbalanced number of formats for xxx.arp when use PGDSpider transformation.

Therefore, for my vcf file, I only kept A, T, C, and G. The number for each sample in xxx.arp after PGDSpider transformation is then equal.

If you do not understand why GC, GT or GCT, GCG happen rather than C, T for GC, GT or T, G for GCT, GCG happen. Please my another post here: How to keep only Biallelic SNP in vcf

Best of luck