Hi there, I'm having an issue with mpileup reporting all zeros for QUAL. My BAM is aligned and sorted with BWA, against hg38 reference. Base and read quality scores look acceptable in IGV.
samtools mpileup -uvB -t DP -f ref.fa -r chrX:48,902,600-48,902,700 mapped_sorted.bam gives me CHROM POS ID REF ALT QUAL chrX 48902600 . C <X> 0 ... one for every base in the specified range here's a variant position: chrX 48902688 . A C,<X> 0 Base phred quality scores as reported in IGV range from 20-40 and read mapping quality is all 60. Any ideas? Thanks! Also posted as a question on https://www.biostars.org/p/145292/#145403 and http://seqanswers.com/forums/showthread.php?p=174195#post174195
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