Open lovelycatZ opened 5 months ago
You seem to miss a reference file. Please specify reference fasta with the -r option.
Hi, thanks for the quick response!
The -r option doesn't seem matter, the problem is that I have changed the script run_CNVnator.pl
to provide an interface for the bin size of CNVnator, but I forgot to set the type for it. Now I have solved.
For CNVnator, it works with or without the reference genome for the BAM file.
Hi, when I run the script
run_CNVnator.pl
for one sample namedXH1006.bam
, there were some errors in theXH1006.histgram.log
file processing data byCNVnator
. But when I provided the same parameters as before and runCNVnator
alone against the same sample, it worked very well. I really struggled with this problem. Below is the error file and running code:/data/xiangxd/project/software/callers/MOPline_1.8.2/scripts/run_SVcallers/run_CNVnator.pl -b XH1006.sort.mkdup.realign.bam -p XH1006 -rd root -build 38 -g MOPline-1.8.2/Data/gap.b38.bed -cp cnvnator -nh 0.
XH1006.histgram.log