Closed alvaralmstedt closed 5 years ago
Solved. The issue was that the GenomeSize.xml I had generated for my hs37d5 reference had "Unknown" for all of the chromosomes in the "type" field. It worked after I changed 1..22 to "Autosome" as well as X and Y to "Allosome".
Hi!
I'm a bit confused about my output. I'm getting CNV calls in all chromosomes except X & Y using my current pipeline as described here (both in CNV.vcf.gz CNV.CoverageAndVariantFrequency.txt):
Issue 97
I suspect that the problem is the vcfs im using for the --ploidy-vcf flag. I am currently using the "placeholder" vcf described in this issue (only changing chrY to Y etc.):
Issue 89
I am doing this because when I try to use the normal vcf (the same one I'm using for the --sample-b-allele-vcf flag) I get the following crash:
Does the --ploidy-vcf need to be formatted in some special way like the GT flag be replaced by CN? Although i suspect that getting no calls in the sex chromosomes using the placeholder vcfs is not indeded behaviour either way.
Thankful for any assistance!