ploid or diploid in vcf for human?

Question

[Dayna]

Hi everybody

It is a naive question coz my background is CS. Should i use ploidy or diploid parameter for generating vcf for human exome data?

[WouterDeCoster]

Does that mean you are doing variant calling using GATK or similar? Ploidy = 2, or diploid, is the same.

[Dayna]

yes doing variant calling. But using samtools and bcftools, so it is different in this pipleine. I will run both pipelines. I wanna know what should be used in human?

Answer 1

[WouterDeCoster]

Humans are mostly diploid, with exception of sex chromosomes and mitochondrial genome.

[Dayna]

Thanks WouterDeCoster so much