is any way to convert an assembly of a genome in contigs to vcf file (variant call format) ??
I have some genomes in fastq (illumina) format and I'm trying to make an analyses similar to this page https://grunwaldlab.github.io/Population_Genetics_in_R/gbs_analysis.html
with my files it's not a problem, using the next pipelines I can convert the fastq files (Forward and Reverse) into VCF files:
bwa index -a bwtsw ref.fasta
samtools faidx ref.fasta
bwa mem ref.fasta r1.fastq r2.fastq > reads.sam
samtools view -b -S -o reads.bam reads.sam
samtools sort reads.bam > reads_sorted.bam samtools index reads_sorted.bam
for single file
samtools mpileup -uf ref.fasta reads_sorted.bam | bcftools call -mv > reads_raw.vcf
or multiples files
samtools mpileup -uf ref.fasta F1_sorted.bam F2_sorted.bam F3_sorted.bam | bcftools call -mv > all_raw.vcf
my problem is that I want to include in the analyses extra genomes assembly (Reference genomes, in contigs) obtained from Genbank in fasta format. is any way to convert the contigs in fasta format to VCF files ????
