Why are we using -B 3 (tumor mismatch penalty)?

We should have more information on why we're doing that.
I do believe it's a good idea, but can we back it up?
https://github.com/nf-core/sarek/blob/05c6e0b63251af83b9e7d5b259cec9e679fccf57/main.nf#L673-L681

	extra = status == 1 ? "-B 3" : ""
	convertToFastq = hasExtension(inputFile1, "bam") ? "gatk --java-options -Xmx${task.memory.toGiga()}g SamToFastq --INPUT=${inputFile1} --FASTQ=/dev/stdout --INTERLEAVE=true --NON_PF=true \| \\" : ""
	input = hasExtension(inputFile1, "bam") ? "-p /dev/stdin - 2> >(tee ${inputFile1}.bwa.stderr.log >&2)" : "${inputFile1} ${inputFile2}"
	"""
	${convertToFastq}
	bwa mem -K 100000000 -R \"${readGroup}\" ${extra} -t ${task.cpus} -M ${fasta} \
	${input} \| \
	samtools sort --threads ${task.cpus} -m 2G - > ${idSample}_${idRun}.bam
	"""

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Why are we using -B 3 (tumor mismatch penalty)? #62

maxulysse
openedon Nov 6, 2019

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Why are we using -B 3 (tumor mismatch penalty)? #62

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maxulysseopenedon Nov 6, 2019

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