I am using PennCNV to call CNVs for Illumina BovineHD datasets as below:
detect_cnv.pl -test -hmm $hmm -pfb $pfb --lastchr 29 -gcmodel $gc $input -log sampleall.log -out sampleall.rawcnv
where,
$hmm <- hhall.hmm file provided by PennCNV
$pfb <- generated for my own population, based on 'compile_pfb.pl' script
$gc <- gc model generated using 'cal_gc_snp.pl'
$input <- input data
Unfortunately, I encountered an error message: Unable to adjust LRR values by GC model due to lack of GCWF measure
I don't know whether this information will help, but the input file for 'cal_gc_snp.pl', 'gc5Base.txt' is not available currently for the reference genome I am using (UCD_ARS1.2), so I made the input file myself, with some help from UCSC bioinformaticians. I can add the detail of how I did if need be.
Could you please explain me how can I solve this problem?
Many thanks in advance! :)
Dear dr. Wang,
I am using PennCNV to call CNVs for Illumina BovineHD datasets as below: detect_cnv.pl -test -hmm $hmm -pfb $pfb --lastchr 29 -gcmodel $gc $input -log sampleall.log -out sampleall.rawcnv
where, $hmm <- hhall.hmm file provided by PennCNV $pfb <- generated for my own population, based on 'compile_pfb.pl' script $gc <- gc model generated using 'cal_gc_snp.pl' $input <- input data
Unfortunately, I encountered an error message: Unable to adjust LRR values by GC model due to lack of GCWF measure
I don't know whether this information will help, but the input file for 'cal_gc_snp.pl', 'gc5Base.txt' is not available currently for the reference genome I am using (UCD_ARS1.2), so I made the input file myself, with some help from UCSC bioinformaticians. I can add the detail of how I did if need be.
Could you please explain me how can I solve this problem? Many thanks in advance! :)
Lim