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Hi,
I am trying to call allelic CN values. I have a Mutect2 VCF, but I also have a curated list of germline SNVs that I got by filtering the Mutect2 VCF. I am wondering how to properly use either …
vymao updated
3 years ago
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Can SCmut be adapted to calling SNVs from scWGS (single-cell whole-genome sequencing)?
Are their any parameter should be changed or we can use it directly?
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Following variant passed as autosomal recessive
from pedigree we have proband 0|1 Mother 0|1 and father 0/0 could you explain how pedigree genotypes are taking into account for variant filtering fo…
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Hi Adam,
I got an empty bam file after addsnv.py. The command is :
`addsnv.py --varfile simu_snv_sites.txt --bamfile simu_N.bam --reference ucsc.hg19.fasta --procs 12 --maxdepth 4000 --cover…
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```
[richel@sens2021565-bianca NSPHS_data]$ wc *.bim --lines
14651585 NSPHS.WGS.hg38.plink1.bim
```
The file does not contain a header
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I would suggest that in addition to the number of subclones per patient, also get the CCF and # of SNVs in each subclone for later use. It's ok if you want to open an issue and do it in another PR tho…
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Using Filezilla
Connection: mississippi.snv.jussieu.fr ; user drosofff@gmail.com ; password ********; port 21
works fine:
`Statut : Résolution de l'adresse de mississippi.snv.jussieu.fr
S…
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Hello. Thank you for developing and sharing iGDA. While testing it out, I noticed a few features that could make it more useful to end-users, in case you decide to do additional development on iGDA.
…