If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:
b) Exact command used:
/app/Genome/gatk-22.214.171.124/gatk GenomicsDBImport -V PBG-467-18-2_S10.vcf.gz -V PBG-415-18_S7.vcf.gz --genomicsdb-workspace-path genomicBDC522_hffh --java-options "-DGATK_STACKTRACE_ON_USER_EXCEPTION=true" -L chr17:41197577-41276148
c) Entire error log:
11:32:54.959 INFO GenomicsDBImport - Importing batch 1 with 2 samples
11:32:54.998 erro NativeGenomicsDB - pid=26649 tid=26687 conflicting field description in the vid JSON and the VCF header of file: PBG_415_18_stream
terminate called after throwing an instance of 'std::exception'
when i import g.vcf to GenomicDB I got the previous error, error shown only when I use g.vcf that were generated from miseq reporter of illumina. but when I use g.vcf from haplotype caller the process work fine.
I used different workspace for illumina files , so I dont merge between two platform files.
- second question , can I import vcf only to GenomicDB not g.vcf or it will initiate an issue later?
- also want to ask if there is a way to convert nextera-manfest of illumina to list-interval to be read by gatk genomicdb.
If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?
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