how to call variants in haploid genome

Question

[itsmesmb]

Hi good people here,

I have a haploid genome (phase)for 40 individuals

e.g.,

 1.  individual1.haploid1.fasta + its index file
 2.  individual2.haploid1.fasta + its index file
              :                            :
              :                            :

 40. individual40.haploid40.fasta + index file

Please can you advise

1. how to call variants and which are the best tools?
2. is it necessary to align each fasta file before calling variants?

Apology, I know my questions are too basic but please please pardon me

Thank you very much

Answer 1

[raphael.B]

Hello, you can do this using GATK Haplotype Caller using the --sample-ploidy option.

[itsmesmb]

thank you so much

[itsmesmb]

Thank you very much, that was very helpful