CalculateContamination (doc)
how many fractions of reads are coming from cross-sample contamination?
- {sample}.pileupsummaries.table -> {sample}.contamination.table
rule calculate_contamination:
input:
# Required arguments.
pileup_summaries = '{sample}.pileupsummaries.table',
# Optional arguments. Omit unused files.
output:
'{sample}.contamination.table'
params:
java_options = '-Xmx4g',
extra = ''
threads: 1
resources: RAM = 4
log: 'logs/gatk/calculate-contamination/{sample}.log'
wrapper:
'http://dohlee-bio.info:9193/gatk/qc/calculate-contamination'