Call Somatic/Germline structural variants using Manta This function takes a pair of matched samples or single | multiple germline variants and calls variants on them. Variant calling mode is established based on wether tumor_bam is provided or not.
1 2 3 4 5 6 7 8 9 10 11 | call_sv_manta(
bin_path = "tools/manta-1.6.0/build/bin/configManta.py",
tumor_bam = "",
normal_bam = "",
ref_genome = "",
output_dir = "",
patient_id = "",
verbose = FALSE,
targeted = FALSE,
threads = 3
)
|
bin_path |
REQUIRED Path to strelka binary. Somatic or Germline. |
tumor_bam |
REQUIRED Path to tumor bam file. |
normal_bam |
OPTIONAL Path to normal samples bam files. |
ref_genome |
REQUIRED Path to reference genome. |
output_dir |
OPTIONAL Path to the output directory. |
patient_id |
OPTIONAL Patient ID to name files after. If not given tumor_bam file name will be used, and if this is not given then normal_bam file will be used. |
verbose |
DEFAULT==FALSE Enables progress messages. |
targeted |
OPTIONAL If exome/capture method. Default FALSE |
threads |
OPTIONAL Number of threads per job. Default 3 |
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