How can I generate VCF file with two different assembled genome fasta?

Question

[kgwkk2]

When I generate VCF file by pair of illumina sequence fastq files with reference assembled genome fasta file, I used BWA mem to assemble illumina fragment and PICARD to remove duplicates. And finally I used gatk4 haplotypecaller for VCF.

But I don't know how to generate VCF file by assembled genome fasta with reference assembled genome fasta. Is there any recommended pipeline to do this?

[WouterDeCoster]

I used BWA mem to assemble illumina fragment

BWA is an aligner, not an assembler.

by assembled genome fasta with reference assembled genome fasta

You will have to explain this a little more. It is highly unclear what you have and what you want.

[kgwkk2]

I apologize for unclear question. I want to compare same species, different strain genomes by making each genome's VCF file. And type strain was used for standard genome for reference(https://www.ncbi.nlm.nih.gov/assembly/GCF_014117465.1). In case of illumina short read sequences (raw data, fastq), I could align short reads based on reference genome, and make BAM file for VCF analysis. But in case of some genome, there were only completely assembled genomic fasta available. I want to make similar form of VCF files from these assembled genomic fasta with reference genome.

Shortly, I want to compare VCF from illumina sequence and VCF from assembled genome equal position as possible.

[Pierre Lindenbaum]

But I don't know how to generate VCF file by assembled genome fasta with reference assembled genome fasta

it's not clear to me.

so your previous question was solved ? What is the major problem with this pipeline of SNPs analysis? . Go and validate the answer. (green tick on the left)

[barslmn]

You can use a nf-core pipeline like sarek. https://nf-co.re/sarek