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GATK at some point started printing the reference contig md5s in the bam header. This is great.
@SQ SN:chr1 LN:248956422 AS:38 M5:6aef897c3d6ff0c78aff06ac189178dd UR:/seq/reference…
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### bug reports
hi guys :
Hi all, when I run gatk (version: 4.5.0.0) CombineGVCFs to combine 240 8 ploidy samples gvcf, it reports the error as below
![image](https://github.com/broadinst…
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Hi Chris,
I am trying to extract variants from a gvcf file and convert to a vcf file. When I run the extract_variants tool on a single sample gvcf everything works fine. But whenever I try to run i…
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Hello, I am trying to construct a tree using the VCF file obtained from merging with GATK and bcftools. After using the VCF2Dis command to generate a .mat file, but there are many '-nan' in the result…
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Hi,
I'm getting the following error when trying to joint call some gVCF files:
```
[14707] [2023-11-09 18:40:20.654] [GLnexus] [error] mother_snv.g.vcf.gz Invalid: allele is not a DNA sequence (…
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### Description of the bug
i don not know why there are such errors
### Command used and terminal output
```
Caused by:
Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_C…
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Howdy,
I am running the following command to genotype a short read to a reference and I get the "invalid BGZF file: does not end in proper EOF marker" error. I haven't edited any of the files since…
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I think the bug that has been found in the CF grant is actually occurring during GVCF creation (wasn't 100% clear to me that was the case, but it sounded like it). Also, I'm pretty sure that this is g…
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Hi,
GATK4 allows to specify custom boundaries for the GQ slices used to group consecutive non-variant positions into a non-variant block, with --gvcf-gq-bands . This feature is quite useful IMO, as…
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I have combined some GVCFs by GenomicsDBImport, and continuity added other samples. however, I find some mistakes with previous samples, how to delete these samples from GATK GenomicsDBImport?