Error running Control-FREEC on WXS data

[danro9685]

Description of the bug

Dear @FriederikeHanssen,

I am experiencing problems running Control-FREEC on my WXS data from matched normal/tumor samples.
I have used sarek on the same samples to perform mutations and structural variants calling and everything works fine.
This is the full command I am using: nextflow run nf-core/sarek -profile conda --input samplesheet.csv --outdir results --wes true --tools controlfreec --trim_fastq true --save_mapped true --save_output_as_bam true --genome GATK.GRCh38 --cf_chrom_len Homo_sapiens_assembly38.len
The error with Control-FREEC is the following: ERROR: there was a problem in the initial guess of the polynomial. Please contact the support team of change your input parameters. Exit. I am attaching a screenshot:

It seems that the problem might be with the bed file used by sarek, as only a small number of SNPs are considered, similarly to what reported here: BoevaLab/FREEC#123
I am also attaching a zip file with the Homo_sapiens_assembly38.len file and the file used in the analysis. additional_files.zip

Any advice on how to fix this issue?

Thank you,
Daniele

Command used and terminal output

nextflow run nf-core/sarek -profile conda --input samplesheet.csv --outdir results --wes true --tools controlfreec --trim_fastq true --save_mapped true --save_output_as_bam true --genome GATK.GRCh38 --cf_chrom_len Homo_sapiens_assembly38.len

Relevant files

No response

System information

No response

[danro9685]

Dear sarek developers,

I was wondering if you might have any advise to fix my issue.

Thanks,
Daniele