Hi
I have been running NGScheckmate on paired tumor-normal samples, first using
ngscheckmate_fastq to generate the vaf files, and then the vaf_ncm.py script to perform the correlations. The issue is coming from the ngscheckmate_fastq step. Some of the vaf files appear to be incomplete, with no header. They don’t cause any issue with the downstrean pearson correlation, but they are dropped from the _all.txt file without any warning or error message. Here's an example of one of the files:
head -n 20 MoHQ-CM-1-178-3_MOHYR2Run64-2DT.vaf
20609 NA NA NA
20610 NA NA NA
20611 NA NA NA
20612 NA NA NA
20613 21 0 0.000000
20614 NA NA NA
20615 NA NA NA
20616 NA NA NA
20617 79 0 0.000000
20618 39 0 0.000000
20619 NA NA NA
20620 NA NA NA
20621 NA NA NA
20622 61 0 0.000000
20623 NA NA NA
20624 65 0 0.000000
20625 NA NA NA
20626 37 0 0.000000
20627 NA NA NA
20628 0 81 1.000000
I've run 1000's of other fastq files from the same project, with the same commands with no issues, but there are ~20 samples with incomplete vaf files.
Hi
I have been running NGScheckmate on paired tumor-normal samples, first using
ngscheckmate_fastq to generate the vaf files, and then the vaf_ncm.py script to perform the correlations. The issue is coming from the ngscheckmate_fastq step. Some of the vaf files appear to be incomplete, with no header. They don’t cause any issue with the downstrean pearson correlation, but they are dropped from the _all.txt file without any warning or error message. Here's an example of one of the files:
I've run 1000's of other fastq files from the same project, with the same commands with no issues, but there are ~20 samples with incomplete vaf files.