Calling SNPs from segregating populations

[maivantan]

Dear Everyone,
I am doing NGS of F2 populations.
But in manual, I saw only for homozygous either parents.
Anyone know how to call SNPs for parent 1, parent 2 and offspring?
Thank you very much

[maivantan]

Dear All,
My understand about genotype in VCF format are correct?

0- allele from reference
1- For the first allele listed in ALT
2- For the second allele listed in ALT
and so on.
0/1, 1/2, 2/1, 1/0, 2/0 are heterozygous?
1/1 is homozygous for allele 1 (parent 1)?
2/2 is homozygous for allele 2 (parent 2)?
0/0 is homozygous for reference?

Thank you

[sarvidsson]

Basically correct, with the following extension:

1/1 is homozygous for allele 1 (parent 1, if parent 1 contained the first allele listed in ALT)
2/2 is homozygous for allele 2 (parent 2, if parent 2 contained the second allele listed in ALT)

[maivantan]

Thank you very much Sarvidsson.

[dpryan]

0/1, 1/2, 2/1, 1/0, 2/0 are heterozygous?

Correct

1/1 is homozygous for allele 1 (parent 1)?
2/2 is homozygous for allele 2 (parent 2)?

There's no guarantee that allele 1 is from parent 1 and 2 is from parent 2 unless your variant caller explicitly states this. Often allele 1 will just be the most frequent, or the alphabetically first.

0/0 is homozygous for reference?

Correct

[maivantan]

I am clear now.
Thank you very much Dpryan.