I have a bam file and would like to know all different allele counts at every position - not only the positions got called for variants, and for each position, I want the counts for all alleles shown up. By reading some previous posts: Vcf - Showing Data For Non-Variant Positions As Well As Snps and Is There A Samtools/Bcftools Setting To Call Variants No Matter How Infrequent? , I figured my code as the following:
samtools mpileup -q 1 -uf $REF $SAMPLE.sort.rudup.bam -t DP,DV,DPR,DP4,SP > $SAMPLE.vc.bcf
but then when I try to get a vcf (bcftools view -c $SAMPLE.vc.bcf > $SAMPLE.vc.vcf), it gave me error: incorrect number of fields (6 != 5) at 0:0
I figured I might miss something important here as I'm new to samtools and bcftools. I would appreciate any help. Thank you in advance!