Open hurleyLi opened 3 years ago
I can't think of a way to bypass it currently. Is one contig list at least a prefix of the other? I could see handling that case (as long as you give it the longer ones first). It uses htslib's name<->integer mapping internally, so I'd otherwise be reluctant to introduce the possibility of inconsistent mappings somewhere in the codebase.
I tried both ways (putting the ones with the extra hs37d5 contig either before or after), and neither one works. I this the error message is clear at least
Invalid: Incompatible gVCF. The reference contigs must match the database configuration exactly.
I guess the only way is to change the header to make the two datasets match?
Hi Mlin!
Thank you for your efforts. Were you able to fix this issue? I'm encountering a similar error in my work on targeted genes. For example, in one sample, I have chromosomes chr1, chr2, chr3, while in another sample, chr3 might be missing.
Thanks!
Hi @mlin I want to merge two big sets of gvcf files, one set has the contig of
hs37d5
, the other don't. When I tried to run glnexus_cli, I got the following error:The loading runs fine until the program sees a samples with different contigs.
I'm wondering if there is any easy way to specify the contigs that needs to be loaded, or somehow bypass this validation procedure. Previously I just add / remove the different contig names from the gvcf file, but this project is kind of big with ~10k samples from each set...
Any suggestions would be appreciated!
This might be related to #236
Thanks! Hurley