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grunwaldlab / krisp

A lightweight kmer-based algorithm for designing diagnostic CRISPR assays using genome data.
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KeyError: 'invalid FORMAT: GQ' #29

Open Janehol opened 4 months ago

Janehol commented 4 months ago

Hi! I'm quite new to bioinformatics and I'm running into an issue using krisp_vcf where I get the following error:

(py311) Janehol@bcsumx01:~/krisp$ krisp_vcf krisp_metadata.csv Race_1.masked.fa --vcf merged_DNAs.vcf.gz --groups NA2 --out_csv krisp_clade2_diagnostic_variants.csv Traceback (most recent call last): File "/home/Janehol/data/miniconda3/envs/py311/bin/krisp_vcf", line 8, in sys.exit(main()) ^^^^^^ File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 1393, in main run_all() File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 1383, in run_all for result in report_diag_region(args.vcf, contig, groups, reference, args, File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 1193, in report_diag_region for region in find_diag_region(variants, groups, reference, kwargs): File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 791, in find_diag_region for region in windower: File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 204, in sliding_window for index, variant in enumerate(variants): File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 196, in from_vcf out = cls(var, groups, check_groups=False, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 162, in init count_data = self._sample_counts(variant, self.groups, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 405, in _sample_counts output = cls._subset_sample_counts(variant, samples, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 391, in _subset_sample_counts is_good = {s: variant.samples[s]['DP'] is not None ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/Janehol/genomics/2-MISC-BY-USER/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 393, in and variant.samples[s]['GQ'] is not None


  File "pysam/libcbcf.pyx", line 3541, in pysam.libcbcf.VariantRecordSample.__getitem__
  File "pysam/libcbcf.pyx", line 813, in pysam.libcbcf.bcf_format_get_value
KeyError: 'invalid FORMAT: GQ'

The VCF file I am using was previously filtered for a minGQ of 20 and has calls for variants with GQ values and some calls with no GQ values (below is an example of one of the samples):
 scaffold_1      1       .       G       .       111     .       MQ0F=0;MQ=30;DP=8;DP4=8,0,0,0;ADF=3;ADR=0;AD=3;AN=14    GT:DP:SP:ADF:ADR:AD

Is the VCF file the issue or am I doing something wrong? Any advice would be greatly appreciated!
cahuparo commented 1 month ago

@Janehol, krisp_vcf can take an unfiltered vcf. What variant caller are you using?