Entering edit mode
3.7 years ago
ilante
▴
30
I am reproducing Manta run as seen in the logs of illumina basespace RNA-Seq Alignment tool v1.1.1 :
[LOG][2021-03-12 20:58:56.377]03/12/2021,20:58:56.193,Launch process: \
/path_to_RNA_Tools/bin/python \
'/path_to_RNA_Tools/Manta/bin/configManta.py' \
--rna --normalBam='path_to_alignments/alignments.bam' \
--runDir='path_to_samples/CTR/replicates/CTR/MantaFusions/manta.run' \
--referenceFasta='/path_to_genomes/genome.fa' \
--config '/opt/illumina/Isis/2.6.25.18/Workflows/WholeGenomeRnaSeqWorker/scripts/configManta.py.ini'
The file shown in the line above configManta.py.ini
is however no were to be found.
The Manta user guide states in the linked section
Options listed in the file:
${MANTA_INSTALL_PATH}/bin/configManta.py.ini
The files are however missing. I am using Manta version 1.6.0 from bioconda.
Your insights will be much appreciated!