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Hi, I noticed that when lifting over variants of the type `ALT=T,*` those are converted into variants of the type `ATL=T,T`, independently of the base in the first ALT that in this example is `T`.
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Dear Sheikhizadeh,
I was wondering whether you are still working on the variant annotation functionality as it would be very interesting!
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+ Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02200-2
https://doi.org/…
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1.dada2 的 chimera killing 功能 看能不加進去
2."multiplex_cpDNAbarcode_clean.txt" 這個 應該要當成一個變數 傳進去 比較對
3."log_dada2.txt" 應該要跟其他result files 放一起比較合理
4.可能有人 不 清楚 要先cd 去那裏執行 powerbarcoder.sh,最好全都改寫成傳參寫法的絕對路徑
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When loading e.g. the below gzipped fasta file:
hgdownload.cse.ucsc.edu/goldenPath/dp3/bigZips/dp3.fa.gz
I get:
```python
fasta = pyfastx.Fasta('./data/genomes/dp3.fa.gz')
RuntimeError: get seq…
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**1. What were you trying to do?**
I am trying to reproduce the steps described in `https://github.com/cgroza/personalized_genomes_gbio/issues/1`, however, after I built the vcf file, and use `…
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First off, the only way I have found that actually works to incorporate custom data is to explicitly add records to config.json and recompile the app: no "custom data (mounted files)" appears as an op…
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Hi,
my name is Jordi and I want to use the file svpop-truth-baseline.vcf.gz from https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=vgsv2019/vcfs/
But I dont know how it has …
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Hi,
I'm trying to align an assembly to minigraph cactus using the command below. However I get the following error:
GraphAligner -g hprc-v1.1-mc-chm13.gfa -f XXX.fasta.gz -a {output} -t …
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Dear,
I have used vep to annotate snv file based on T2T CHM13 V2.0. Firstly, I have only used chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz, and the command line is :
vep --database 0 --dir_plugi…