https://github.com/simonsfoundation/remap2b38
Remap a bam file to a given reference, and call variants with a choice of GATK HaplotypeCaller, Freebayes, Platypus.
https://github.com/simonsfoundation/remap2b38
Last synced: 11 months ago
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Remap a bam file to a given reference, and call variants with a choice of GATK HaplotypeCaller, Freebayes, Platypus.
- Host: GitHub
- URL: https://github.com/simonsfoundation/remap2b38
- Owner: simonsfoundation
- License: mit
- Created: 2017-08-14T15:40:40.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2017-08-22T20:05:52.000Z (almost 9 years ago)
- Last Synced: 2025-01-18T21:32:28.260Z (over 1 year ago)
- Language: Shell
- Homepage:
- Size: 11.7 KB
- Stars: 0
- Watchers: 4
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## *remap2b38*
### Overview
*remap2b38* contains one script *remap.sh* that can be used to remap a bam file to
a new reference genome, and to call variants with a choice of GATK HaplotypeCaller,
Freebayes, and Platypus using [*pipeline*](https://github.com/simonsfoundation/pipeline.git).
The following steps will be executed.
1. samtools collate
2. samtools fastq
3. bwa mem
3. sambamba sort
4. sambamba markdup
5. GATK base quality recalibrate
6. sambamba index
7. Call variants using pipeline
If you do not wish to call variants, comment out pipe04.sh call.
### Dependences.
[*samtools*](http://www.htslib.org) and [*sambamba*](http://lomereiter.github.io/sambamba/) must be in your $PATH.
Clone *pipeline*.
```
cd ~
git clone https://github.com/simonsfoundation/pipeline.git
```
Clone this repo
```
cd ~
git clone https://github.com/simonsfoundation/remap2b38.git
```
Run
```
~/remap2b38/remap.sh \
bam_prefix \ # eg 123, if bam(s) are 123*.bam
/path/to/iput_bams_dir/ \ # directory containing files defined by the prefix
scr \ # tmp/scr/work defines working dir, see comments in remap.sh
/path/to/output_dir/ \ # output directory (will be created)
1 \ # 1/0 remove working_dir/do not remove
8 \ # use this many cores
/path/to/include_hg38.mk \ # e.g. ~/pipeline/ppln/include_hg38.mk, if you followed instructions above
/path/to/pipeline/ppln \ # e.g. ~/, if you followed instructions above
> /path/to/log_file.log 2>&1
```