I am new to DNA sequence analysis, especially variant calling. I had some sequence data and used bwa to perform the alignment. After I had sam file from bwa, I use samtools and bcftools to perform variant calling. However, when I more the final vcf file, I don't see the AC key-value pairs in the vcf file. I cannot calculate the frequency of alleles at each locus. Would anyone have an idea about what I should do?
My purpose is to find the allele frequencies at each locus. If there are other methods to do this, please give me a help. Thank you.
In fact, when I view the sorted bam file, I can see the alignment and the reference. It looks fine.
I tried the following commands in my workflow:
samtools mpileup -g -f ref.fa short_reads_aligned.sorted.bam > short_reads_variants.bcf
bcftools view -c -v short_reads_variants.bcf > short_reads_variants.vcf
I also tried the following
samtools mpileup -uf ref.fa short_reads_aligned.sorted.bam | bcftools view -bvcg - > var.raw.bcf bcftools view var.raw.bcf > var.flt.vcf
Thanks in advance C