Laura Gauthier
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Hi Matt Johnson The provided WGS calling intervals split at Ns in the reference so there are no boundary effects. However in hg38 there are fewer and fewer of those. In our production pipeline, w...
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The recommended file for hg38 exomes is gs://gatk-sv-resources-public/gcnv-exome/contig_ploidy_prior_hg38.tsv. The ploidy_prior columns refer to the copy number of the contig of interest and the v...
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Hi Wei-Yang BAI, There is no DRAGEN mode for joint calling -- it's only single-sample VCF or GVCF. You can run our best practices for joint calling on DRAGEN GVCFs for most DRAGEN versions, but a f...
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Hi Dahn-young Dong, No-call doesn't really have a strict definition, but I would agree that anything with no depth is worth excluding. I'd recommend you trust DP over genotype call. To calculate s...
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Hi Yifei Dai, I'd recommend the same pipeline for low pass WGS. That's what we've been running since the low pass 1000 Genomes days. The main caveat is that you'll want to NOT run ReblockGVCF or ...
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Hi user105689, The picard code says If this interval is in the opposite orientation, all alleles and genotypes will be reverse complemented and indels will be left-aligned. I don't see any explici...
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Hi Shashank Shekhar Padhi, This has been an issue since the beginning of time and I can suggest a variety of workarounds. If you're really intent on having a single VCF file, then you'll need to f...
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P.S. I think you change those Ns to the actual reference base at that position if you supply a reference fasta with the -R argument. N is showing up in the REF column of the VCF and I expect the I...
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Hi Adriana! It looks like I was the one who added those to the GCNV segments VCF header. :-) PostprocessGermlineCNVCalls also gets used in the GCNV joint calling pipeline, which is where those an...
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We talked about this offline, but I think it's worth documenting here for posterity (especially since the old forum with the hit you found is disappearing.) Our joint calling pipeline only runs in ...