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Hi.
I have been trying to use GLnexus with a list of gvcfs. I have tried all different ways to point to the vcfs with a vcf on each line and I keep getting the following error when running via DNAn…
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We need to review what https://nf-co.re/sarek can do to determine:
- if it could be used as is
- if it could be used with modifications
- if we'd rather extract and replicate some functionality h…
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Here is a snippet of a CGI-Var file:
```
1265 2 all chr1 68316 68543 ref = =
1266 2 all chr1 68543…
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My dear
How to do variant calling in multi samples?
does it to get gvcf file and merge it ?
how to merge the gvcf file?
thankyou!
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I tried to merge the trios' gvcf files which generate by DeepVariant and the command and error message show like below:
`./glnexus_cli --config DeepVariantWES --bed exon.bed HY20080095.gvcf HY20080…
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Hi @mlin
I want to merge two big sets of gvcf files, one set has the contig of `hs37d5`, the other don't. When I tried to run glnexus_cli, I got the following error:
```
[7451] [2020-09-24 17:19…
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I have a population of 200 individuals, and I know that I can generate VCFs using VG calls. But I want to know how to merge the generation into GVCF, which includes all sample variation information.
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Platypus should be able to produce gVCFs for many individual samples, and then merge them to create a single VCF with appropriate genotypes across all samples. This is an alternative to joint calling …
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Hi. Am trying out the codes. Understand that the raw files here mean genotype files from DTC companies. However, what I have is only vcf and gvcf files from in-house sequencing platform. May I know ca…
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It appears that it was decided to deprecate INFO/END, without any public discussion (https://github.com/samtools/hts-specs/commit/97b26a1da5b8f511dba70dfcec953d17813e54f0)
Although I see the advant…