Support scripts for the sanger somatic workflows.
Using python3, run pip install -r requirements.txt
Extracts the brass VCF and renames TUMOUR to TUMOR. The final outputs are a bgzipped vcf and its index.
extract_brass_vcf.py -h
[INFO] [20190710 15:11:25] [extract_brass_vcf] - --------------------------------------------------------------------------------
[INFO] [20190710 15:11:25] [extract_brass_vcf] - extract_brass_vcf.py
[INFO] [20190710 15:11:25] [extract_brass_vcf] - Program Args: scripts/extract_brass_vcf.py -h
[INFO] [20190710 15:11:25] [extract_brass_vcf] - --------------------------------------------------------------------------------
usage: Utility for extracting brass files from sanger results archive.
[-h] --results_archive RESULTS_ARCHIVE --output_prefix OUTPUT_PREFIX
optional arguments:
-h, --help show this help message and exit
--results_archive RESULTS_ARCHIVE
Sanger results tar archive.
--output_prefix OUTPUT_PREFIX
Prefix for all outputs.
Extracts the caveman VCF and renames TUMOUR to TUMOR. The final outputs are a bgzipped vcf and its index.
extract_caveman_vcf.py -h
[INFO] [20190710 15:11:25] [extract_caveman_vcf] - --------------------------------------------------------------------------------
[INFO] [20190710 15:11:25] [extract_caveman_vcf] - extract_caveman_vcf.py
[INFO] [20190710 15:11:25] [extract_caveman_vcf] - Program Args: scripts/extract_caveman_vcf.py -h
[INFO] [20190710 15:11:25] [extract_caveman_vcf] - --------------------------------------------------------------------------------
usage: Utility for extracting caveman files from sanger results archive.
[-h] --results_archive RESULTS_ARCHIVE --output_prefix OUTPUT_PREFIX
optional arguments:
-h, --help show this help message and exit
--results_archive RESULTS_ARCHIVE
Sanger results tar archive.
--output_prefix OUTPUT_PREFIX
Prefix for all outputs.
Extracts the Pindel VCF and renames TUMOUR to TUMOR. The final outputs are a bgzipped vcf and its index.
extract_pindel_vcf.py -h
[INFO] [20190715 15:19:48] [extract_pindel_vcf] - --------------------------------------------------------------------------------
[INFO] [20190715 15:19:48] [extract_pindel_vcf] - extract_pindel_vcf.py
[INFO] [20190715 15:19:48] [extract_pindel_vcf] - Program Args: scripts/extract_pindel_vcf.py -h
[INFO] [20190715 15:19:48] [extract_pindel_vcf] - --------------------------------------------------------------------------------
usage: Utility for extracting pindel files from sanger results archive.
[-h] --results_archive RESULTS_ARCHIVE --output_prefix OUTPUT_PREFIX
optional arguments:
-h, --help show this help message and exit
--results_archive RESULTS_ARCHIVE
Sanger results tar archive.
--output_prefix OUTPUT_PREFIX
Prefix for all outputs.
Extracts the caveman copynumber file from the ASCAT directory and reformats it to the GDC standard. Extracts two values from the ASCAT samplestatistics file and prints them to stdout.
[INFO] [20190711 18:21:39] [extract_ascat] - --------------------------------------------------------------------------------
[INFO] [20190711 18:21:39] [extract_ascat] - extract_ascat.py
[INFO] [20190711 18:21:39] [extract_ascat] - Program Args: scripts/extract_ascat.py -h
[INFO] [20190711 18:21:39] [extract_ascat] - --------------------------------------------------------------------------------
usage: extract_ascat.py [-h] {reformat_copynumber,extract_stats} ...
Tool to process Sanger WGS pipeline TAR output and produce GDC standard files
and metrics.
positional arguments:
{reformat_copynumber,extract_stats}
optional arguments:
-h, --help show this help message and exit
[INFO] [20190711 18:22:07] [extract_ascat] - --------------------------------------------------------------------------------
[INFO] [20190711 18:22:07] [extract_ascat] - extract_ascat.py
[INFO] [20190711 18:22:07] [extract_ascat] - Program Args: scripts/extract_ascat.py reformat_copynumber -h
[INFO] [20190711 18:22:07] [extract_ascat] - --------------------------------------------------------------------------------
usage: extract_ascat.py reformat_copynumber [-h] [--input INPUT]
[--output OUTPUT]
[--gdcaliquot GDCALIQUOT]
optional arguments:
-h, --help show this help message and exit
--input INPUT, -i INPUT
path to file output from Sanger pipeline
--output OUTPUT, -o OUTPUT
path for output file
--gdcaliquot GDCALIQUOT, -g GDCALIQUOT
GDC Aliquot ID used to generate the file
[INFO] [20190711 18:22:34] [extract_ascat] - --------------------------------------------------------------------------------
[INFO] [20190711 18:22:34] [extract_ascat] - extract_ascat.py
[INFO] [20190711 18:22:34] [extract_ascat] - Program Args: scripts/extract_ascat.py extract_stats -h
[INFO] [20190711 18:22:34] [extract_ascat] - --------------------------------------------------------------------------------
usage: extract_ascat.py extract_stats [-h] [--input INPUT]
optional arguments:
-h, --help show this help message and exit
--input INPUT, -i INPUT
path to file output from Sanger pipeline
Extracts the brass bedpe file, formats the header and outputs bgzipped + tabix indexed file.
extract_brass_bedpe.py -h
[INFO] [20190712 16:15:18] [extract_brass_bedpe] - --------------------------------------------------------------------------------
[INFO] [20190712 16:15:18] [extract_brass_bedpe] - extract_brass_bedpe.py
[INFO] [20190712 16:15:18] [extract_brass_bedpe] - Program Args: extract_brass_bedpe.py -h
[INFO] [20190712 16:15:18] [extract_brass_bedpe] - --------------------------------------------------------------------------------
usage: Utility for extracting brass bedpe file from sanger results archive.
[-h] --results_archive RESULTS_ARCHIVE --output_prefix OUTPUT_PREFIX
optional arguments:
-h, --help show this help message and exit
--results_archive RESULTS_ARCHIVE
Sanger results tar archive.
--output_prefix OUTPUT_PREFIX
Prefix for all outputs.