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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