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Klinische Genetica
capture-lumc
hutspot
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f6db48a6
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f6db48a6
authored
7 years ago
by
Sander Bollen
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Fix typos in README
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5f9751a9
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f6db48a6
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@@ -5,7 +5,7 @@ GATK HaplotypeCaller.
## Features
*
Any number of samples is supported
*
Whole-genome calling, regardless of
sample protocol used.
*
Whole-genome calling, regardless of
wet-lab library preparation.
*
Follows modern best practices
*
Each sample is individually called as as a GVCF.
*
A multisample VCF is then produced by genotyping the collection of GVCFs.
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@@ -115,7 +115,7 @@ The following configuration values are **required**:
| ------------- | ----------- |
|
`OUT_DIR`
| Absolute path to output directory |
|
`REFERENCE`
| Absolute path to fasta file |
|
`SAMPLE_CONFIG`
| Path to config file as descrbed above |
|
`SAMPLE_CONFIG`
| Path to config file as descr
i
bed above |
|
`GATK`
| Path to GATK jar.
**Must**
be version 3.7 |
|
`DBSNP`
| Path to dbSNP VCF |
|
`ONETHOUSAND`
| Path to 1000Genomes VCF |
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@@ -188,7 +188,7 @@ more complex, as nearly all rules are duplicated by sample and some
(the scatter jobs) additionally by chunk.
As a rough estimate of the total number of jobs in pipeline you can use
the followig formula:
the followi
n
g formula:
```
math
jobs = 4+(21*n_{samples})+(1*n_{samples}*n_{beds})+(1*n_{samples}*n_{chunks})+(1*n_{chunks})
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