Exclamation mark in Samtools mpileup output
1
1
Entering edit mode
20 months ago
pr ▴ 10

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 • 451 views
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4
Entering edit mode
20 months ago
gb ★ 2.0k

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mpileup is originally made to call variants.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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