vcf2maf not converting missing AD values to 0

[edoyango]

Hi,

We're looking at using vcf2maf to prepare our VCF files for import into cBioPortal, but I've run into the issue:

$ python3 vcf2maf.py -i ../vcf-noann-FTatleast1PASS/solace2-0003.vcf --tumor-id tumour --normal-id germline
Loading data from file: ../vcf-noann-FTatleast1PASS/solace2-0003.vcf
Traceback (most recent call last):
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/vcf2maf.py", line 1640, in <module>
    main()
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/venv/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/venv/lib/python3.11/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/venv/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/venv/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/vcf2maf.py", line 1628, in main
    generate_maf_from_input_data(
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/vcf2maf.py", line 1552, in generate_maf_from_input_data
    maf_data = extract_vcf_data_from_file(
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/vcf2maf.py", line 1496, in extract_vcf_data_from_file
    maf_record = create_maf_record_from_vcf(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/vcf2maf.py", line 1048, in create_maf_record_from_vcf
    resolve_vcf_counts_data(
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/vcf2maf.py", line 630, in resolve_vcf_counts_data
    (t_ref_count, t_alt_count, t_depth) = resolve_vcf_allele_depth_values(
                                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/vast/projects/staffordfox-cbioportal/genome-nexus_annotation-tools/vcf2maf.py", line 511, in resolve_vcf_allele_depth_values
    mapped_sample_format_data["DP"] = str(sum(map(float, allele_depth_values)))
                                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: could not convert string to float: ''

I believe this is because .,237 is the AD value, and the . is being converted to an empty string, which is not accepted by float. I've traced this back to line 341.

        # attempt to parse values as int - if not an int then set value to empty string
        allele_depth_values = []
        for value in mapped_sample_format_data["AD"].split(","):
            if is_valid_integer(value):
                allele_depth_values.append(value)
            else:
                allele_depth_values.append("")

Should "0" be appended instead of ""? For our data, this would make sense.

Please let me know how best to resolve this, and I will create a pull request.