Generate VCF from fastq
$ smake.py [OPTIONS] COMMAND [ARGS]Smake scans a directory containing fastqs. Smake creates:
- a Makefile which can be used to create one (multisample) VCF from fastqs, depending on information given by the user (sample names)
- a SMakefile which save this information to avoid having to give it again for subsequent uses.
The scan command is required before using regenerate and list commands.
In order to add new fastqs to the analysis, scan command is required.
| Options | Description |
|---|---|
| --full | Performs a full scan, ignoring existing Makefile. Exclusive with --update and --ask |
| --update | Perform a partial scan, updating existing Makefile. Exclusive with --full and --ask |
| --ask | Ask whether to perform a full scan or an update. Exclusive with --full and --ask (default) |
| -o, --output | Path to the Makefile to generate (default: in the scanned directory) |
| --help | Show this help and exit |
Example:
$ smake.py scan --full FastqDirectory/ -o MakefileThe regenerate command renegerates the Makefile using information kept in the SMakefile.
This command is used if:
- the Makefile has been manually edited
- the Makefile has been damaged
- Smake has been updated
| Options | Description |
|---|---|
| --full | Performs a full scan, ignoring existing Makefile |
| --update | Perform a partial scan, updating existing Makefile |
| --ask | Ask whether to perform a full scan or an update (default) |
| --help | Show this help and exit |
Example:
$ smake.py regenerate MakefileThe list command shows all the targets in the Makefile. These targets can be passed as parameter to gmake.
| Options | Description |
|---|---|
| --help | Show this help and exit |
Example:
$ smake.py list Makefile- smake.py: main program
- smake: symbolic link to py3wrapper
- _smake: autocomplete for zsh
- Makefile.tpl: template for Makefile to generate by smake.py
- SMakefile.tpl: template for SMakefile to generate a Makefile with annotations concerning samples
- py3wrapper: in order to use python3 on a python2 machine
Performs set manipulations on variants (inclusions and / or exclusions of variants from a VCF in another VCF).
$ vcfsetop.py [OPTIONS] COMMAND [ARGS]The filter command filter variants from a VCF file (stdin if the argument is "-"), to keep only variants from the required samples (if any), from the included samples (otherwise) and not from the excluded samples (anyway).
| Options | Description |
|---|---|
| -e, --exclude | Drop variants from this sample |
| -i, --included | Keep variants from this sample |
| -r, --require | Keep variants from this sample only |
| --xgi / --no-xgi | Expand unknown genotypes for included samples (default: no) |
| --xge / --no-xge | Expand unknown genotypes for excluded samples (default: no) |
| --help | Show this help and exit |
Example:
$ vcfsetop filter -r Sample1 -r Sample2 -e Sample3 input.vcf > output.vcfThis command keeps common variants in Sample1 and Sample2, and excludes variants in Sample3. Samples should be in a same VCF file in input.
The list command list sample that can be used to filter variants from a VCF file using the filter command.
| --help | Show this help and exit |
|---|
Example:
$ vcfsetop list input.vcf- vcfsetop.py: main program
- vcfsetop: symbolic link to py3wrapper
- vcfsetop: autocomplete for zsh
- py3wrapper: in order to use python3 on a python2 machine