Hi, thanks for this amazing to call copy number alterations in NGS data.
I run facets on WGS data with around 60X in tumor and 40X in non tumors samples and I noticed an issue concerning males samples on the chrX:
Indeed, if the sample correspond to a male, I can observe that the number of point drastically drop in chrX compared to other chromosomes, probably because the ndepth is too stringent for the coverage associated to chromosome X when the number of genomic material is divided by two in the library, compared to others chromosomes.
As an example I attached two chromosomes (chrX and chr8), with the same parameters on the same sample. Of note, snp.nbhd = 200, ndepth = 35, min.nhet = 10, cval (preProcSample) = 25, cval (procSample) = 350.
Do you know a solution to take in account the gender of a sample in the processing of chromosome X?
Hi, thanks for this amazing to call copy number alterations in NGS data.
I run facets on WGS data with around 60X in tumor and 40X in non tumors samples and I noticed an issue concerning males samples on the chrX: Indeed, if the sample correspond to a male, I can observe that the number of point drastically drop in chrX compared to other chromosomes, probably because the ndepth is too stringent for the coverage associated to chromosome X when the number of genomic material is divided by two in the library, compared to others chromosomes.
As an example I attached two chromosomes (chrX and chr8), with the same parameters on the same sample. Of note, snp.nbhd = 200, ndepth = 35, min.nhet = 10, cval (preProcSample) = 25, cval (procSample) = 350.
Do you know a solution to take in account the gender of a sample in the processing of chromosome X?
Best regards, Quentin