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.