If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Germline CNV output
Hi GATK Team,
I am testing the Germline-CNV-Tools. In the tools documentation of PostprocessGermlineCNVCalls it is stated, that "... CNV call is either < DEL > or ...". In my genotyped_segments output file there is "N" as REF and "<DEL,DUP>" as ALT. Here is one example line:
chr2 26414098 CNV_chr2_26414098_179423395 N < DEL>,<DUP> . . END=179423395 GT:CN:NP:QA:QS:QSE:QSS 0:2:376:56:3077:175:267
I used the following parameters:
gatk PostprocessGermlineCNVCalls --calls-shard-path 1446-18_GCNV-calls/ --model-shard-path /media/Berechnungen/AnnotationDBs/CNV/Exom_neu/Exom_GCNV-model/ --sample-index 0 --autosomal-ref-copy-number 2 --allosomal-contig chrX --allosomal-contig chrY --output-genotyped-intervals 1446-18.genotyped_intervals.vcf --output-genotyped-segments 1446-18.genotyped_segments.vcf --contig-ploidy-calls 1446-18_DGCP-calls/
Why is my reference Tag "N" and not 2? Is there any error in my parameters?
Thanks in advance