Thank you! This appears to be what I'm looking for but I receive the following error, which I've shortened as it is enough to get the idea:
A USER ERROR has occurred: Input files reference and reads have incompatible contigs: Dictionary reference is missing contigs found in dictionary reads. Missing contigs:
chrUn_KN707606v1_decoy, chrUn_KN707607v1_decoy, chrUn_KN707608v1_decoy, chrUn_KN707609v1_decoy, chrUn_KN707610v1_decoy, chrUn_KN707611v1_decoy, chrUn_KN707612v1_decoy, chrUn_KN707613v1_decoy, chrUn_KN707614v1_decoy, chrUn_KN707615v1_decoy, chrUn_KN707616v1_decoy, chrUn_KN707617v1_decoy, chrUn_KN707618v1_decoy, chrUn_KN707619v1_decoy, chrUn_KN707620v1_decoy, chrUn_KN707621v1_decoy,
The testing company provided, in both the VCF files -- and apparently the CRAM files -- certain "odd chromosome values" which I have no idea the significance of. I expect chr1,chr2,chr3,chr4,chrX,chrY, etc. but the above values also exist in my data and, because the reference fasta apparently does not, this error is returned. My sample data is all GRCh38.
Am I correct in presuming this is benign as the data behind these "missing contigs" may not be relevant anyway? If so, is there any way I can force the command to proceed, and ignore that error?
To be clear as to what reference file I am using, I am using GCA_000001405.15_GRCh38_no_alt_analysis_set.fa from https://hgdownload.soe.ucsc.edu/treehouse/reference/
With both the index file (.fai) and dictionary file (.dict) from there downloaded into the same directory.
I appreciate any insight you can provide. Thanks again
Here is the logic for doing joing calling of SNP: https://gatk.broadinstitute.org/hc/en-us/articles/360035890431-The-logic-of-joint-calling-for-germline-short-variants