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Using blacklist in sarek pipeline

Hi, I need to measure tumour mutational burden in a set of samples. The plan would be to perform variant calling using the sarek pipeline. I have found a list of blacklisted regions in the mouse genome (mm10) (https://www.encodeproject.org/files/ENCFF547MET/) but I do not know how to incorporate it into the pipeline. The current pipeline looks something like this

nextflow run nf-core/sarek \
    --input sarek_sample_sheet.csv \
    --outdir results \
    --genome mm10 \
    --skip_tools baserecalibrator \
    --tools mutect2,freebayes \
    -profile x \
    -r 3.6.1 \
    -resume

Would anybody be able to suggest how to use a blacklist in sarek? Thanks!

sarek tmb
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by giacomo.bregni • giacomo.bregni

1 answer

https://nf-co.re/sarek/3.7.1/parameters/

use --intervals

just create a BED file for your whole genome and use "bedtools subtract" to remove the blacklisted.bed

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written by Pierre Lindenbaum Pierre Lindenbaum

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