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CAG-CNV / ParseCNV2

Parse Copy Number Variation from Array and Sequencing
GNU General Public License v3.0
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Statistics Header Values= ERROR: No P column header. #3

Open JoannaTan opened 1 year ago

JoannaTan commented 1 year ago

I tried to run parseCNV2 using the following command

perl ParseCNV2.pl -i myfile.rawcnv -q mytrait.qt -m 1 -d 2 -p 1 -b hg19

but i get the error message 'ERROR: No P column header.'

I tried running the example command and the files given, and i also get the same error message

perl ParseCNV2.pl -i Cases.rawcnv -q Cases.qt -m 1 -d 2 -p 1 -b hg19 -batch ID_Category.txt

joeglessner1 commented 1 year ago

Apologies for my delayed reply. I expanded out the range of rare variant test statistics for response to reviewers but a side effect is that <-stat fisher> must be specified in the commands for default similar to the original ParseCNV or <-stat logistic> or the other options. For these small test files, -no_freq needs to be added so all the SNPs don't end up filtered out or with P=NA. If you capture the on screen output, there is a line "Statistics Header Values=" that will show your headers, the P column is required and can be any of these {P,PVALUE,P-VALUE,PVALUETWOSIDE} case insensitive. To keep the 5 test runs separate log files, use -o TEST1 for example. Variant IDs in the input VCF (column 3) need to have unique values, not just "." (I just uploaded a fixed version of v4.3.vcf).