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# This is an example pipeline specification to do multi-sample variant calling
# with the Platypus variant caller. Each input is preprocessed by aligning
# against a reference genome (defaults to GRCH38), fixing mate information, and
# marking duplicates. Finally platypus is called over all samples.
{bionix ? import <bionix> {}
,nixpkgs ? import <nixpkgs> {}
,inputs
,ref ? null}:
with bionix;
let
preprocess = f:
samtools.markdup {}
(samtools.sort {}
(samtools.fixmate {}
(bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;} f)));
in platypus.call {} (map preprocess inputs)
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