Commit e33b4498 authored by van den Berg's avatar van den Berg
Browse files

Add an option to restrict BaseRecalibration

The base recalibration (BQSR) step of the pipeline can take up to 7 hours for
WGS samples, which is a significant part of the total run time.

The developers of GATK state that BQSR requires at least 100M bases per read
group: "We usually expect to see more than 100M bases per read group; as a rule
of thumb, larger numbers will work better."

A human WGS sample with an average read depth of 43x has almost 1300 times that
amount of bases. The analysis of these samples would be sped up greatly by
restricting BQSR to a single chromosome.
parent 095305f0
Pipeline #4012 passed with stages
in 38 minutes and 35 seconds
{
"samples": {
"micro": {
"read_groups": {
"lib_01": {
"R1": "tests/data/fastq/micro_R1.fq.gz",
"R2": "tests/data/fastq/micro_R2.fq.gz"
}
}
}
},
"reference":"tests/data/reference/ref.fa",
"dbsnp": "tests/data/reference/database.vcf.gz",
"known_sites": ["tests/data/reference/database.vcf.gz"],
"restrict_BQSR": "chrM"
}
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