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Hi qing,
I'm new to bioinformatics and I'm wondering how other users get the list of SNVs? I'm analyzing data from mouse and I could download dbSNPs information from UCSC. Thanks for your time!
Be…
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Hi,
I split the 1000GP chrX VCF into nonPAR, PAR1, and PAR2 regions then tried creating .msav files with these but I encountered some issues. Below is the code I used.
```bash
#/usr/bin/env bas…
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Hi Team,
I tried this package using the same input as with signature.tools.lib. The SNV catalogue is generated from tabToSNVcatalogue, and the ID catalogue is generated by SigProfilerMatrixGenerato…
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Hello, guoweilong! Thank you for your tool!
I tried to call SNVs from ATCGmap file with 'bayes' option as in the tutorial:
`cgmaptools snv -m bayes --bayes-dynamicP -i file1.ATCGmap -v file1.vcf`
a…
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I used strelka2 somatic to detect snv. An important SNV is marked as "LowDepth", and here is the variant in ./results/variants/somatic.snvs.vcf.gz:
```
chr4 66361261 . A G …
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The MEI view currently only has overlapping SVs.
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* Input:
[input.txt](https://github.com/genome-nexus/annotation-tools/files/5859875/input.txt)
* Intermediate files: `annotation-tools` intermediate files I must add the .txt at the end or github…
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* input: [input.txt](https://github.com/genome-nexus/annotation-tools/files/5859860/input.txt)
* Intermediate files: `annotation-tools` intermediate files I must add the .txt at the end or github …
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Hi, I'm new to pyclone and I would like to use it to inferring AML clonal architecture from tumor-only targeted DNA sequencing samples.
I'm not sure how to get information about major and minor c…
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The `mirtop.tsv` output contains repeated rows for some isomiRs with identical first 12 columns:
```
UID Read miRNA Variant iso_5p iso_3p iso_add3p iso_snp iso_5p_nt iso_3p_nt iso_add3p_…