Question: Output all allele counts at each position using bcftools
0
gravatar for DVA
3.5 years ago by
DVA530
United States
DVA530 wrote:

Hello,

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!

samtools bcftools • 1.9k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by DVA530
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