Why is samtools mpileup reporting all zero quality scores?

[fwuffy]

Hi everyone.

I'm calling some variants using samtools 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


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.

Anyone run into this before?

Thanks!

[lindenb]

cross posted : https://www.biostars.org/p/145292/

[fwuffy]

cross posted : https://www.biostars.org/p/145292/

Hope that's ok.

[Brian Bushnell]

Hope that's ok.

It's just helpful to note it when you post (at each location), so that people can check to see if it's already been answered sufficiently before writing a potentially quite long answer. Furthermore, it helps others who subsequently find the thread by searching.

[fwuffy]

As an update, this is only happening on chr X. Other chromosomes have proper QUAL values.
Edit- actually that was confusion on my part. It's happening on all chromosomes. Still no clue as to why, but bcftools call finds quality scores from mpileup output (presumably from data in the INFO fields) and populates that QUAL column.