No DP in VCF getting error when using kirsp_vcf

[buchanri]

Hello, I have a vcf that I'm wanting to try krisp_vcf on. Here's the command I used with the paths to the input files. My vcf doesnt have DP or GQ information.

krisp_vcf /nfs7/BPP/Chang_Lab/buchanri/agro_crispr_dx/data/krisp_vcf/BV1_vs_BV2_pangenome_vcf_test_2.csv /nfs7/BPP/Chang_Lab/buchanri/agro_crispr_dx/data/fna_assemblies/CA75-95_BV2_NA_T4c_renamed.fna --vcf /nfs7/BPP/Chang_Lab/buchanri/agro_crispr_dx/results/pangenome/BV1_BV2/98_10000_25000_BV1_BV2_nf_pangenome/vg_deconstruct/BV1_and_BV2_pansn_renamed.fasta.gz.gfaffix.unchop.Ygs.view.gfa.JL5177_BV2_fixed.vcf --groups BV1 BV2 --out_csv /nfs7/BPP/Chang_Lab/buchanri/agro_crispr_dx/results/krisp_vcf/pangenome_BV1_BV2/BV1_BV2_nf_pangenome_out.csv --out_align /nfs7/BPP/Chang_Lab/buchanri/agro_crispr_dx/results/krisp_vcf/pangenome_BV1_BV2/BV1_BV2_nf_pangenome_align.txt

Here's the error I'm getting:

Traceback (most recent call last):
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/bin/krisp_vcf", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/krisp_vcf.py", line 1393, in main
    run_all()
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/krisp_vcf.py", line 1383, in run_all
    for result in report_diag_region(args.vcf, contig, groups, reference, args,
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/krisp_vcf.py", line 1193, in report_diag_region
    for region in find_diag_region(variants, groups, reference, **kwargs):
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/krisp_vcf.py", line 791, in find_diag_region
    for region in windower:
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/krisp_vcf.py", line 204, in sliding_window
    for index, variant in enumerate(variants):
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/find_diag_var.py", line 198, in from_vcf
    out = cls(var, groups, check_groups=True, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/find_diag_var.py", line 162, in __init__
    count_data = self._sample_counts(variant, self.groups,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/find_diag_var.py", line 406, in _sample_counts
    output = cls._subset_sample_counts(variant, samples,
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nfs7/BPP/Chang_Lab/buchanri/miniforge3/envs/krisp_env/lib/python3.12/site-packages/krisp/krisp_vcf/find_diag_var.py", line 392, in _subset_sample_counts
    is_good = {s: variant.samples[s]['DP'] is not None
                  ~~~~~~~~~~~~~~~~~~^^^^^^
  File "pysam/libcbcf.pyx", line 3537, in pysam.libcbcf.VariantRecordSample.__getitem__
  File "pysam/libcbcf.pyx", line 813, in pysam.libcbcf.bcf_format_get_value
KeyError: 'invalid FORMAT: DP'