NGSCheckMate
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parklab
Software program for checking sample matching for NGS data
Hi, RNAseq and WES data of the sample were measured. I was able to successfully use your tool to detect sample mislabelling ; i checked the result with two methods...
Hello, thanks for writing NGSCheckMate! There seems to be an issue when using Python 3.9.7 to run the tool. The error I get is: File "/Users/u0149445/Desktop/variant_calling/NGSCheckMate/ncm_test.py", line 66 link =...
Hi all, I am trying to run NGSCheckMate on paired normal-tumour samples. It seems to be running the samtools mpileup fine, and producing the appropriate vcf files. However, I received...
Hello, How to prepare the input BED file ? I just get the common SNP site betwen 2 samples as a input, and the result was similar with your bed...
Hi, thank you for this amazing tool! I would like to implement this for other species (e.g. mice) using the fastq module. I can't seem to find a documentation about...
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...
Hello, I have an application to run ngscheckmate iteratively on the same dataset when new data is added. It is easiest for me to use the fastq file workflow but...
File "ncm.py", line 61, in pearson_def return diffprod / math.sqrt(xdiff2 * ydiff2) ZeroDivisionError: float division by zero when passing 2 vcfs that are very similar. Here are x and y...
bcftools should now be used instead of samtools mpileup. Docs need to be updated.
