mpileup -B option

[giverny]

Hi there
I used mpileup with the -B option to predict variations. To evaluate our pipeline, the same analysis has been done by an other lab and results have been validated in wet lab.
we share true positive prediction... good. But also we missed A LOT of true positive. I checked without the -B option and they are found. A lot of reads were not considered by using -B ... and it was wrong to do that
I'm wondering if you know which parameters I can play with to be less stringent.
Thanks for your time

[swbarnes2]

That's my experience too. Real, sanger validated SNPs will turn up with -B is selected, but won't be called otherwise.

Here's the result running

../../../../samtools/1.14/samtools mpileup -f ../1/genome6.fa region.bam > mpileup_noB.txt
598255 C 136 t,ttttttT.tttt.ttTTT.ntnn.t.t.,t.,,.TTTTtT..Tttt,T.tTtttTT.tttttttttTT.t,ttttt,t.T...tTTTtTTtttt.tT.TtTTTT.TTT.Tt,.ttttt,TtTTTt,ttttTTT^Ft !U!!!!!!!g!!>!B!!!%!BE!BDf!h!ag!hhYh!!!!!!h]*!!!f0g!%!!!!!Z!!!!!!!!!!>g!c!$!!!h!f!hhh!!!!!,!!!!!h!!g!%!!!$h!!!h!$BS!!>!!g!!!!!!b#!!!!!!!

../../../../samtools/1.14/samtools mpileup -Bf ../1/genome6.fa region.bam > mpileup_B.txt

598255 C 136 t,ttttttT.tttt.ttTTT.ntnn.t.t.,t.,,.TTTTtT..Tttt,T.tTtttTT.tttttttttTT.t,ttttt,t.T...tTTTtTTtttt.tT.TtTTTT.TTT.Tt,.ttttt,TtTTTt,ttttTTT^Ft ggThghghfghgBfBghh^dBEhBDfdhhagghhYhfgfdhgh]WffffPgf]fhggcZdfghhffhhgBghcg_hhchgfghhhefghgThPhafhfdgh^a`hZhfghhe_BS`gBghghghhhhg]hdhgfgf

the -B has for some reason destroyed the quality scores of the letters in this area, and the vcf is empty in this region. When I make it starting with -B, then that SNP pops up.

It's mixed, but the sanger was plain as day.