Exclamation mark in Samtools mpileup output

Question

[pr]

Hi, I used samtools to generate a mpileup file. In the base column, I notice some "!". I sought out the sigification in domcumentation/already asked question and haven't find their meaning. Does anybody know?

Exemple:

FNXXX 2595 T 1 ^!a J

Answer 1

[gb]

Try to add -Bx to your command.

Short story long:

mpileup is originally made to call variants. To not count the overlapping bases between the forward and reverse reads twice samtools changes the quality score to "!". This "!" has a phred score of 0 and will be ignored in the variant calling process.

Here more info: https://sourceforge.net/p/samtools/mailman/message/32793789/