Hello, every one!

When I do QTL-seq analysis, the vcf file I get after using bcftools for SNP calling and filter does not have AD (alele depth) field inside. I don't know what's wrong with my code, please help me out, thanks!

Here is my codes:

bcftools snp calling codes:

bcftools mpileup /public/home/gguo/qtlseq/markup_results/merged_bam/*bam --fasta-ref /public/home/gguo/qtlseq/ref_genome/S_lycopersicum_chromosomes.3.00.fa | bcftools call -mv -o raw.vcf

bcftools snp filtering codes:

bcftools view --types snps -m 2 -M 2 -q 0.05:minor raw.vcf | bgzip -c > filtered_raw.vcf.gz