Min Quality differes between iVar and mpileup

[svarona]

Description of the bug

Use the same min Quality for the IVAR and for the mpileup for masking:

viralrecon/conf/modules_illumina.config

Line 376 in 687bca3

: '-t 0.25 -q 20 -m 10'

viralrecon/conf/modules_illumina.config

Line 672 in 687bca3

ext.args = "-a --ignore-overlaps --count-orphans --no-BAQ --max-depth 0 --min-BQ 0"

Command used and terminal output

Relevant files

No response

System information

No response