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Commit 761517da authored by vvanoost's avatar vvanoost
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add filtering step of reads based on mapping quality >=2

parent b1dcaa1f
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......@@ -33,6 +33,9 @@ profiles {
$mapping_fastq {
container = "bowtie2:2.3.4.1"
}
$quality_filtered_bam {
container = "samtools:1.7"
}
$sort_bam {
container = "samtools:1.7"
}
......@@ -132,6 +135,9 @@ profiles {
$mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
$quality_filtered_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
$sort_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
......
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