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 <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?
What is the meaning of options
-vin mpileup command?
Neither affect the reported quality score
what version samtools are you using? (and have you tried updating to the latest version?)
1.131-25 which is the latest. Just downloaded.
Actually it may be 1.1 only, will have to verify this ... thanks.
edit: It's 1.1.?. I'm going to try the develop branch
This is mac OS x, and compiling from source is throwing some errors. I think this is a pre-compiled version for OS x
Not sure if that includes exact minor version or not
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=59422
This is typically not recommended as it runs the risk of annoying people in both communities.
You may want to make a small BAM file of just this region and then send an email to the samtools list. This looks a bit like a bug, given the MAPQ and Phred scores you have.