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parklab / NGSCheckMate

Software program for checking sample matching for NGS data
MIT License
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VCF files to use #25

Open plbngl opened 5 years ago

plbngl commented 5 years ago

Hello! I want to compare the genotype of 10 different samples obtained from either snp arrays and ATAC seq to check for sample swaps. For each of the 10 samples I have one VCF from the array and one from samtools mpileup from ATAC seq. I also have bed file with ~50.000 variants that I selected to be in high coverage peaks and polymorphic. I tried to run your program on these 20 vfcs but I got this error:

python $NCM_HOME/ncm.py -V -f -d sample_swap/sample_vcfs/ -O sample_swap/ -bed sample_swap/min20cov_snps.bed

Generate Data Set from sample_swap/sample_vcfs/ using this bed file : sample_swap/min20cov_snps.bed Traceback (most recent call last): File "/home/pbenaglio/NGSCheckMate/ncm.py", line 1460, in createDataSetFromDir(base_dir,bedFile) File "/home/pbenaglio/NGSCheckMate/ncm.py", line 220, in createDataSetFromDir real_depth[file] = depth[file] / float(real_count[file]) ZeroDivisionError: float division by zero

I wonder if it is possible to use vcf files from array data at all?

Thank you very much, Best, Paola

shannjiang commented 3 years ago

Hi I got the same error but from different line: Traceback (most recent call last): File "/sc/arion/projects/H_PBG/scripts/NGSCheckMate/ncm.py", line 1470, in createDataSetFromList(base_list,bedFile) File "/sc/arion/projects/H_PBG/scripts/NGSCheckMate/ncm.py", line 403, in createDataSetFromList real_depth[file] = depth[file] / float(real_count[file]) ZeroDivisionError: float division by zero

Have you resolved it finally?