GetPileupSummaries (doc)
get pileup metrics as a table, which is used to infer contamination.
- {sample}.bam, {common_biallelic_variants}.vcf.gz (can be obtained by using SelectVariants with option
--restrict-alleles-to BIALLELIC
) -> {sample}.pileupsummaries.table
rule get_pileup_summaries:
input:
# Required arguments.
bam = '{sample}.bam',
common_biallelic_variants = 'resources/small_exac_common_3.hg38.vcf.gz'
# Optional arguments. Omit unused files.
output:
'{sample}.pileupsummaries.table'
params:
java_options = '-Xmx4g',
extra = '',
threads: 1
resources: RAM = 4
logs: 'logs/gatk/get-pileup-summaries/{sample}.log'
wrapper:
'http://dohlee-bio.info:9193/gatk/coverage/get-pileup-summaries'