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tfwillems / HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
GNU General Public License v2.0
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VCF filtering issue #94

Closed hannah-happ closed 7 months ago

hannah-happ commented 7 months ago

I am trying to filter my HipSTR VCF but am getting the following error:

Traceback (most recent call last): File "/scratch/ucgd/lustre-work/quinlan/u6055472/storage/tools/HipSTR/scripts/filter_vcf.py", line 233, in <module> main() File "/scratch/ucgd/lustre-work/quinlan/u6055472/storage/tools/HipSTR/scripts/filter_vcf.py", line 94, in main vcf_writer = vcf.Writer(sys.stdout, vcf_reader) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/scratch/ucgd/lustre-work/quinlan/u6055472/storage/tools/miniconda3/lib/python3.11/site-packages/vcf/parser.py", line 642, in __init__ self.writer = csv.writer(stream, delimiter="\t", ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

I'm using the default parameters (below), and get the same error with my VCF and the test VCF in the HipSTR test directory

python ${scripts}/filter_vcf.py --vcf ${VCF_DIR}/str_calls.vcf --min-call-qual 0.9 --max-call-flank-indel 0.15 --max-call-stutter 0.15 --min-call-allele-bias -2 --min-call-strand-bias -2

Any suggestions? Thanks!

hannah-happ commented 7 months ago

moving this to the gymrek-lab forked HipSTR