Exclamation mark in Samtools mpileup output

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

bam samtools mpileup mapping

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updated 6.5 years ago by gb

• written 6.5 years ago by pr •

1 answer

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mpileup is originally made to call variants.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/

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written 6.5 years ago by gb

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