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### Description of feature
Hi, I was wondering if you guys have thought to give the pipeline an option to use variants called from a DNA-seq(typically wgs) pipeline to use as input into "ASE read cou…
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Hi, I was wondering if this is an issue that has been seen before. I am new to facets and copy number calling so I would appreciate any help/advice.
I have been running FACETS for several samples …
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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
Would it be possible to view th…
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I was wondering if it could make sense for `cnvkit` to add derived biomarkers such as HRD (integrating loss of heterozygosity (LOH), telomeric-allelic imbalance (TAI), and large-scale state transition…
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Hi,
I'd like to access the chromosomal coordinate and log2 data fields for all segments plotted in dark-orange in the scatter plot output from scatter.py. I noticed that the bins reported in the st…
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Hi Natsuhiko,
Could you explain how reference allele bias can be calculated per SNP? I understand how reference allele bias can be calculated genome-wide per individual by taking the average refere…
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Hello,
Could you point me to a proper VCF to do snp-pileup on WGS for mm10/GRCm38?
I downloaded [00-All.vcf.gz](https://ftp.ncbi.nih.gov/snp/organisms/archive/mouse_10090/VCF/00-All.vcf.gz) but …
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Dear, Venkatraman!
Can't figure out why FACETs infers genome wide 2:0 state for one of my samples (that is highly unlikely to be the case) and finds 2:1 in another very similar (by logOR baseline)…
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for example if an LOH event leads to total copy number 2, minor copy number 0, it is necessary to know which allele has 2 copies and which has 0.
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Hi,
I am also trying to use the unpaired feature of PSCBS as some of the data do not have a matched normal sample. However, I am running into some problems trying to call AB on segment data done us…