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Hey there,
I have done a separate call snp on individual bam using this tool under docker and subsequently merged the vcf files using GLnexus. But I would like to ask if I can do a group call snp on …
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Hi, I am running numbat with mouse snRNAseq data generated by Takara SMART-Seq Stranded Kit. I did analysis on 52 nuclei and got the following error message. Can anyone help to check? The data that I…
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Hi,thank you for developing mgatk.
I have 183 bamfiles from smart-seq2, and I run the code:mgatk call -i ./bamfiles/ -g hg38 -q 30 ;
which does not produce any error and the output files looks good!…
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Uploading vcfs to opencravat seems to result in incorrect parsing of the numeric values (likely parsed as strings), which leads to the hindered filtering
![image](https://user-images.githubuserconten…
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Hello,
I have been facing issues with conda libraries. So, I have installed micromamba and started using using it. For the PacBio workflow. I kept the all the existing rule scripts and directories …
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**1. What were you trying to do?**
I intend to use pggb to obtain a pan-reference genome graph composed of 31 strains of *Bacillus subtilis*, and use vg to obtain **bam files similar to BWA**, and …
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Beginning with sequence-based searches of the literature via PaperBLAST and using the sequences acquired from PomBase, UniProtKB
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**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.5/docs/FAQ.md**: Yes
**Describe the issue:**
I do not understand how Deepvariant decides if there is a call at sites with …
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Enable the pipeline to read the genome assembly from a metadata file
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### What happened?
Thank you for updating the workflow. I am running the workflow epi2me-labs/wf-human-variation 1.4.0 on EPI2ME Labs. I have tried to use the UCSC human reference downloaded from:
…