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Hi, Dr. Song
Thank you for the development of the software anchorwav!I used your software to successfully generate the maf file, such as ler.anchors,ler.f.maf,ler.log,ler.maf, but unfortunately did n…
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Hello, I want to analyse trios data (father,mother,child). Should I create the vcf files for each member with deepvariant and then combine then with GLnexus?
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Is it possible to give gvcfgenotyper a list of chromosome positions to genotype GVCFs at? For example I have two sets of samples joint genotyped using gvcfgenotyper. Some variants are only present i…
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## Discussion \#1
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bshifaw [3:59 PM]
Hi Chris,
The featured joint calling method is using NIO.
https://portal.firecloud.org/#methods/gatk/joint-discovery-gatk4/9/wdl
Is this the method you a…
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Hello,
Thank you for producing the tool. :)
I am wondering why the output includes a gvcf file. How do you think I should use it? Is the gvcf file prepared for the future to detect somatic vari…
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**Cannot access cross account S3 bucket if the bucket has KMS enabled**
**Describe the Bug**
[In the documentation](https://aws.github.io/amazon-genomics-cli/docs/concepts/data/#cross-account-ac…
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I am using Deepvariant to obtain vcf files for single individuals and merge these files with GLnexus. I am having 2 issues.
1) I observed that a 0/0 is coded if an individual is homozygous referenc…
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### Description of the bug
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (
earlycasualcaiman)' …
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When trying to merge VCF and GVCF files using BCF files, "NON-REF" under the ALT field is being considered as a literal instead of a symbolic reference. VCF tools list all "NON-REF" fields in the end …
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This wdl is failing to `Build` with this error - `Context initialization failed due to TypeError: Cannot read property 'i' of undefined.
Wdl can be found here - https://github.com/broadinstitute/wd…