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Thanks a lot for providing this tool!
We often analyse capture data with controlfreec were not all chromosomes from the fai are present in the capture kit. ControlFreec then fails with:
Command output:
Control-FREEC v11.6 : a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data
Multi-threading mode using 2 threads
..consider the sample being male
..Breakpoint threshold for segmentation of copy number profiles is 1.2
..telocenromeric set to 50000
..FREEC is not going to adjust profiles for a possible contamination by normal cells
..Coefficient Of Variation set equal to 0.05
..it will be used to evaluate window size
..Output directory: .
..Directory with files containing chromosome sequences: /Chromosomes
..Sample file: tumor.mpileup
..Sample input format: pileup
..Control file: normal.mpileup
..Input format for the control file: pileup
..forceGCcontentNormalization was set to 1: will use GC-content to normalize the read count data
..minimal expected GC-content (general parameter "minExpectedGC") was set to 0.35
..maximal expected GC-content (general parameter "maxExpectedGC") was set to 0.55
..Polynomial degree for "ReadCount ~ GC-content" normalization is 3 or 4: will try both
..Minimal CNA length (in windows) is 3
..File with chromosome lengths: Homo_sapiens_assembly38.fasta.fai
..File Homo_sapiens_assembly38.fasta.fai was read
Command error:
For example, you can remove chromosome HLA-DRB1*11:01:01 from yourHomo_sapiens_assembly38.fasta.fai
Error: chromosome HLA-DRB1*11:01:02 present in your Homo_sapiens_assembly38.fasta.fai file was not detected in your file with capture regions capture-regions.bed
Please solve this issue and rerun Control-FREEC
This means that we need to adapt the fai or chromosome files everytime, which is not ideal in a workflow/automatic processing setting.
Ideally, we can have a fixed set of reference files and the above error would rather lead to an exclusion of that chromosome.
The text was updated successfully, but these errors were encountered:
Thanks a lot for providing this tool!
We often analyse capture data with controlfreec were not all chromosomes from the
fai
are present in the capture kit. ControlFreec then fails with:This means that we need to adapt the fai or chromosome files everytime, which is not ideal in a workflow/automatic processing setting.
Ideally, we can have a fixed set of reference files and the above error would rather lead to an exclusion of that chromosome.
The text was updated successfully, but these errors were encountered: