blob: 2b63ae2449cdf8ca75461b01d61a3dbe91c36064 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
|
# 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> {}
,inputs
,ref ? null}:
with bionix;
let
preprocess = pipe [
(bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;})
(samtools.fixmate {})
(samtools.sort {})
(samtools.markdup {})
];
in platypus.call {} (map preprocess inputs)
|
