I'm using samtools mpileup and bcftools view to find variants. I'm perplexed why none of the alleles for any of the samples are shown as "missing data" (e.g. "./."). The coverage shouldn't be deep enough nor the samples similar enough for there not to be at least some "missing data". Here's my sample code:
Is there a flag I'm missing or misusing?
This is using samtools version 0.1.19-44428cd and bcftools version 0.1.17-dev (r973:277) on CentOS 6.5 (64-bit).
Code:
samtools mpileup -uf ref.nfa A.bam B.bam C.bam | bcftools view -vcg - > ABC.vcf
This is using samtools version 0.1.19-44428cd and bcftools version 0.1.17-dev (r973:277) on CentOS 6.5 (64-bit).