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My bwa command:
bwa-mem2 mem -M -t 24 -p -R '@RG\tID:SAMN10471711\tSM:SAMN10471711\tLB:SAMN10471711\tPL:ILLUMINA' /group/zhougrp/zhoulab/GENOMES/Chicken/EMBL/version107/GRCg7b/Gallus_gallus.bGalGal1…
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> [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/bio…
mr-c updated
2 months ago
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### Description of the bug
hello I have an error when I ran the nextflow sarek pipeline:
`nextflow -bg run nf-core/sarek -r 3.4.0 -params-file params_samplesheet_F52_3.json -profile docker &
Wo…
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A few options (feel free to add more):
- Continue to use GATK 3.6 CombineVariants in Somatic/Multi-Caller SNV workflows
- Use GATK4 MergeVCFs (or similar) and drop the `set` annotation from any fi…
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### Description of the bug
Hi,
I am getting the following error. Can you please help ?
Thanks
-[nf-core/rnavar] Pipeline completed with errors-
Error executing process > 'NFCORE_RNAVAR:R…
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Hi Nalini,
I was playing around with this package. Thanks a lot providing these R bindings! Much appreciated.
Do you have by any chance an example for iterating through a GATK4 GenomicsDBImport …
lima1 updated
3 years ago
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I'm trying to update gatk4's bioconda recipe to include gcnvkernel (a python package required for gatk4's germline cnv caller). However, when adding gcnvkernel to the requirements and introducing an i…
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Please convert each of this as an issue when you start working on one.
(That can be done by clicking on the circle dot `⊙` at the end of the line in the list below, hover on a list item to see it)
A…
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Whelp, I guess we have to tackle the bull.
First thoughts, we need to work out what nf-core/modules we would need, check what are already available and what we would have to write.
List based on…
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In GATK4's CNV caller, read depth bins and SNP allele frequencies are segmented separately (by CBS and an HMM, respectively), then intersected (like `GenomicArray.cut`) and a final pass compares adjac…