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Hi, Dr Guo,
After running the following command cgmaptools snv -m bayes --bayes-dynamicP -i AK0H.ATCGmap.gz -v filename.VCF, I get an output file containing only header information as follows:
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Hi,
I have a kind of similar issue as in https://github.com/mskcc/vcf2maf/issues/332. I noticed this problem earlier and fixed the non matching names with previous data.
Now I have the problem…
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This seems to happen to a certain extent for the 25 samples I am working with, but here is a specific case:
I am haplotagging a bunch of ~ 14 kb reads. I know the sample in question is heterozygous…
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In the article, I could find the Variant calling methods of SNVs and indels separately.
I found you called SNVs using SAMtools mpileup with mapping quality >20 and base quality >20, but I couldn't fi…
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dear jsming1996：
您好，我在这里使用中文询问
请问关于snv数量矫正的代码在哪一部分，我没能找到，因此在这里想向您直接请教询问
I couldn't find the part of the SNV number correction code, so I would like to ask you directly here
could you please teach…
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Hi,
Can you please teach us a bit about how to navigate through the resulting output? I am aware that each column is reporting a different aspect of an immunological assessment, but is there an eas…
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Hi Qing.
I made a input.vcf containing about 660000 SNVs and about 15% were in dbSNP.
I got an error while running giremi:
```
[mpileup] 1 samples in 1 input files
error:C…
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I have a question regarding rank score penalty points which I assume is due to lack of "good enough" compound.
I found a missense variant and a SV (small deletion) in the gene FBP1 in our case 2433…
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Hi,
In the "All SNVs and INDELs" search option, would it be possible in future updates to add the field corresponding to the Inheritance model in the search results and as a search filter (genetic mo…
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In one approach (fmt="vcf-simple"), use pandas instead of pysam to parse the VCF as a tabular file, but don't further parse the INFO and sample columns. This lets us read an arbitrary VCF, manipulate …