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how to call variants in haploid genome

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

haploid-genome
• 1,414 views • link
written by itsmesmb • itsmesmb

1 answer

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

• 0 views • link
written by raphael.B • raphael.B

Thank you very much, that was very helpful

• 0 views • link
written by itsmesmb • itsmesmb

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