Use of samtools/bcftools vcf file

[vasotola]

Hello, would a vcf file produced with bcftools mpileup and call be appropriate for use with polyRAD? As per the information provided about polyRAD, you state it can take in a vcf file with calculated allelic depths (AD), but only list tassel or gatk as possibilities, not samtools/bcftools. Bcftools mpileup can calculate allelic depths so I'm assuming (and hoping) that would be okay? I am not in the agriculture or model organism world, and this is my first study on a polyploid organism and previously I've always used bcftools and it's worked really well for me, so I'd like to stick with that.

Thanks!
Alex

[lvclark]

I haven't tried it, but I think it would work!

[vasotola]

Okay, awesome, thank you!