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change bcftools output format

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This commit is contained in:
Ramprasad Neethiraj 2022-04-22 11:05:56 +02:00
parent 447b3ee05d
commit 9da85209f2
1 changed files with 2 additions and 2 deletions
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4
conf/pipeline/raredisease/hasta.config
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@ -15,9 +15,9 @@ process {
} }
withName: BCFTOOLS_VIEW { withName: BCFTOOLS_VIEW {
if (params.genome == 'GRCh37') { if (params.genome == 'GRCh37') {
ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "' ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
} else if (params.genome == 'GRCh38') { } else if (params.genome == 'GRCh38') {
ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"' ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
} }
publishDir = [ publishDir = [
enabled: false, enabled: false,