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We are troubleshooting an issue from the GATK forum with CollectVariantCallingMetrics. There seems to be an issue with the user's dbSNP file but the stack trace does not give enough information so tha…
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The [GVCF format](https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format) uses `` as a placeholder for a possible non-reference allele in the ALT column. Becau…
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Hi,
I've been hitting errors when running some tests of germline small variant joint calling with GATK (trying to optimise some parameters for running on our cluster).
First there were I/O error…
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Had working code and now every cwl workflow I try with the post API just returns a 200. Using the API demo code.
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In `CollectVariantCallingMetrics` for GVCF_INPUT, the variant used for counting is sub-contexted from the original variant, with alleles (alts) being filtered by GT field. Similar filtering should be …
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I think a very useful addition would be an option that allows users to calculate PRS with imputation based on the reference allele. As I understand, for all variants not contained in the input VCF, th…
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Currently, GenomicsDBImport has no way to take in large interval/BED files to process the gvcf merging step. One option would be to perform it on individual chromosomes. Will need to investigate more
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## Bug Report
### Affected tool(s) or class(es)
GATK Haplotypecaller
### Affected version(s)
(4.3.0.0 and 4.2.6.1)
### Description
We used Haplotypecaller in GVCF mode (initially in 4.2.…
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For the pipeline we are using Sniffels in it would be really convenient to have genomic vcf support.
Are there any plans to ass gvcf support in the future?
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When I use gatk to CombineGVCFs, the following error occurs: "Cannot read file because no suitable codecs found".
How can I solve this problem?