convert fasta to vcf

Question

[taimur.al-said]

Hi,

I have downloaded full genomes from NCBI in FASTA format. I would like to convert these files in VCF in order to use them for heterozygosity analysis. Since most programs require vcf input files and the known way is to start the conversion process using 2 fastq files for alignment then sam to bam and finally vcf.

Can someone please advise as to what I must do?

Thank you

[barslmn]

Simply, you need to align your reads to reference genome, and then you need to do a variant call. You should search google for resources on how people do these for your specific platform, biologic questions and species.

[taimur.al-said]

Hi lennykovac and barslmn,

Thank you for your responses. I want extract ROH and HET metrics. I have 2 species that are sequenced, my 2 files are in fastq format, converted filtered them to create vcf files and managed to get the metrics i need for my 2 sample files. However, i would like to compare my metrics to sequences available on ncbi in fasta (not fastq) format. Would it be possible to do extract these metrics using fasta files? ill need to convert them to vcf. Thank you.

Answer 1

[lennykovac]

Its a quite complex process and you should know what you are doing in order to understand the output. I can recommend this guide.

Here is a flowchart, that could give you a general idea of the process.