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rule indelrealigner:
input: bam="{base}.bam",intervals="{base}.intervals",bai='{base}.bam.bai'
output: bam=temp("{base}.realigned.bam")
params: batch="-q ccr -l nodes=1:gpfs"
threads: 1
shell: "touch {output}"
rule realignertargetcreator:
input: "{base}.bam", "{base}.bam.bai"
output: temp("{base}.intervals")
params: batch="-q ccr -l nodes=1:gpfs"
threads: 32
shell: "touch {output}"
rule indexbam:
threads: 1
input: '{base}.bam'
output: temp('{base}.bam.bai')
params: batch="-q ccr -l nodes=1:gpfs"
shell: 'touch {output}'
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