I'm calling some variants using samtools (and bcftools) from a bwa aligned and sorted BAM.
For some reason, the samtools mpileup is reporting all zero quality scores, but I know the base and read quality scores in the BAM are good (viewed in IGV)
samtools mpileup -uvB -t DP -f ref.fa -r chrX:48,902,600-48,902,700 mapped_sorted.bam
CHROM POS ID REF ALT QUAL
chrX 48902600 . C
one for every base in the specified range
here's a variant position:
chrX 48902688 . A C,
Base phred quality scores as reported in IGV range from 20-40 and read mapping quality is all 60.
Anyone run into this before?