Too high number of SNPs using ddRAD data (36 cattle)

Question

[ymberzal]

Hello

I have ddRAD data of 36 cattle that I made a vcf file out of using samtools sort, bcftools mpileup and call. The number of SNPs I am getting is very high (in millions). I referred to other articles where ddRAD data was analysed using a similar pipeline but everyone's SNPs were in thousands.

I have checked every step of my pipeline and it looks right. But why are my SNPs three times greater than what everyone else is getting using a similar pipeline?

Please help.

[Michael]

Did they really all use the identical pipeline, or did they maybe use some variant filtration after that? Did they not maybe use GATK or another variant caller instead?

[ymberzal]

Thanks for your reply. Turns out the difference was due to different sets of restriction enzyme used in other studies.