Some errors and question

[yoonicon]

Thank you for your sharing.

I have one question and one error.

First, my question is that whether I can compared somatic mutations of two ALS patient groups. I have two groups of VCF files and can i compared somatic mutation between them.

And second, using SigprofilerExtractor, I met an error, which is "index out of range". Here is my error code.

---

Cell In[13], line 1
----> 1 sig.sigProfilerExtractor('vcf', './example/output', './example', minimum_signatures=1, maximum_signatures=3)

File ~/.local/lib/python3.10/site-packages/SigProfilerExtractor/sigpro.py:542, in sigProfilerExtractor(input_type, output, input_data, reference_genome, opportunity_genome, cosmic_version, context_type, exome, minimum_signatures, maximum_signatures, nmf_replicates, resample, batch_size, cpu, gpu, nmf_init, precision, matrix_normalization, seeds, min_nmf_iterations, max_nmf_iterations, nmf_test_conv, nmf_tolerance, nnls_add_penalty, nnls_remove_penalty, initial_remove_penalty, collapse_to_SBS96, clustering_distance, export_probabilities, make_decomposition_plots, stability, min_stability, combined_stability, allow_stability_drop, get_all_signature_matrices)
539 elif input_type=="vcf":
540 ################################# For vcf input files #######################################################
541 title = project # set the title for plotting
--> 542 data = datadump.SigProfilerMatrixGeneratorFunc(project_name, refgen, project, exome=exome, bed_file=None, chrom_based=False, plot=False, gs=False)
543 # Selecting the MutationType
544 if mtype == ["default"]:

File ~/.local/lib/python3.10/site-packages/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py:470, in SigProfilerMatrixGeneratorFunc(project, genome, vcfFiles, exome, bed_file, chrom_based, plot, tsb_stat, seqInfo, cushion, gs)
466 lines = sorted(lines, key = lambda x: (x[0], int(x[2])))
469 context = '6144'
--> 470 mutation_pd, skipped_mut, total, total_DINUC, mutation_dinuc_pd_all = matGen.catalogue_generator_single (lines, chrom, mutation_pd, mutation_dinuc_pd_all, mutation_types_tsb_context, vcf_path, vcf_path_original, vcf_files, bed_file_path, chrom_path, project, output_matrix, context, exome, genome, ncbi_chrom, functionFlag, bed, bed_ranges, chrom_based, plot, tsb_ref, transcript_path, tsb_stat, seqInfo, gs, log_file)
472 if chrom_based and not exome and not bed:
473 matrices = matGen.matrix_generator (context, output_matrix, project, samples, bias_sort, mutation_pd, exome, mut_types, bed, chrom, functionFlag, plot, tsb_stat)

File ~/.local/lib/python3.10/site-packages/SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGenerator.py:358, in catalogue_generator_single(lines, chrom, mutation_dict, mutation_dinuc_pd_all, mutation_types_tsb_context, vcf_path, vcf_path_original, vcf_files, bed_file_path, chrom_path, project, output_matrix, context, exome, genome, ncbi_chrom, functionFlag, bed, bed_ranges, chrom_based, plot, tsb_ref, transcript_path, tsb_stat, seqInfo, gs, log_file)
355 mut_seq += previous_mut
357 for l in range(start1+1, start2, 1):
--> 358 mnv_seq += tsb_ref[chrom_string[l-1]][1]
359 mut_seq += tsb_ref[chrom_string[l-1]][1]
361 if i < len(mnv_index) -1 :

IndexError: index out of range

Thanks!

[mdbarnesUCSD]

Hi @yoonicon,

Could you please include your JOB_METADATA file?

In regards to comparing the outputs between two different runs, there are various plots that are output that you can use to facilitate your comparisons and the wiki page for SigProfilerExtractor has additional information about these. The TMB plot may be of interest to you.

Thanks!

[mdbarnesUCSD]

Please reopen this issue if you have any further questions.