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Hello Author,
I made vcf including SNV & indels. It seems only SNVs written in ssm_data.txt. Can you suggest me how I change my indel& SV data into phylowgs input?
Thankyou,
James
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Hello author, i am sorry to disturb you. I want to apply SibeliaZ to virus (for example HIV) to obtain collinear blocks. After that, I will extract SNVs from those collinear blocks. However, I found I…
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Add QC flags either to a separate "QC" column or dedicated area for flags.
## Flags
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Hi @FreekManders and everyone,
Is there a way to use MutationalPatterns to get the SNVs correspond to a specific mutational signature?
I assume that the absolute contribution means the number of…
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Hi Qing,
I have some problems when I use the giremi.
The first is the "repeat snv".When I annotated the variations, some point be annotated to 2 more genes.The 2 point are the same position,but the ge…
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(summarizing @arahuja on the subject)
**Simple Version**
When many SNVs are found close together, consider dropping them under the assumption that something may have been wrong with the reads there. …
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Hi,
When using MethylExtract v1.9
It gets
################### Running MethylExtract v1.9 ###################
Functions summary:
Use of uninitialized value $typeFasta in string eq at Met…
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I tried to run the pipeline with a dataset, but had several problems.
Firts I ran the pipeline without adjusting the config, except for the sample annotation file. After that I tried to set `doPer…
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Hello,
I tried to use geva to estimate the ages of some rare variants but got empy output. When checking with the log file, I noticed it saying Position not viable. I am not sure what that means an…