Manta SV caller: Why is the ${MANTA_INSTALL_PATH}/bin/configManta.py.ini file missing?
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7 days ago
ilante • 0

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!

Basespace Manta • 49 views
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