Unable to run COBALT in tumor only mode

[Chunkz616]

Thanks great tool ! Just in tumor only mode I am having issues with it recognising the commands

Set variables

TUMOR="PD59703a" TUMOR_BAM="/lustre/scratch126/casm/team274sb/ah39/DNA_data/sim_links/scLeuk_3.7.24/PD57224a.sample.dupmarked.bam" OUTPUT_DIR="/lustre/scratch126/casm/team274sb/ah39/DNA_data/purple/cobalt_output/${TUMOR}" GC_PROFILE="/lustre/scratch126/casm/team274sb/ah39/DNA_data/sim_links/scLeuk_3.7.24/GC_profile.1000bp.38.cnp" DIPLOID_BED="/lustre/scratch126/casm/team274sb/ah39/DNA_data/sim_links/scLeuk_3.7.24/DiploidRegions.38.bed.gz" THREADS=2 COBALT_JAR="/lustre/scratch125/casm/team274sb/ah39/code_packages/cobalt-1.9.jar"

Run COBALT in tumor-only mode

java -Xmx28G -jar $COBALT_JAR \ -tumor $TUMOR \ -tumor_bam $TUMOR_BAM \ -output_dir $OUTPUT_DIR \ -threads $THREADS \ -gc_profile $GC_PROFILE \ -tumor_only_diploid_bed $DIPLOID_BED

is giving me

15:49:03 - org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -tumor_only_diploid_bed usage: CountBamLinesApplication -gc_profile Location of GC Profile -input_dir Input directory (used for migration only) -min_quality Min quality [10] -output_dir Output directory -ref_genome Path to reference genome fasta file if using CRAM files -reference Name of reference sample -reference_bam Path to reference bam file -threads Number of threads [4] -tumor Name of tumor sample -tumor_bam Path to tumor bam file -validation_stringency SAM validation strategy: STRICT, SILENT, LENIENT [STRICT] (base) ah39@farm22-head1:~/Bash_scripts$

Tried a few different work arounds but seems like it is not expecting -tumor_only_diploid_bed $DIPLOID_BED input. Is there anything I am missing

[Chunkz616]

Apologies, was running in older version - pre-tumor only mode. my bad