-
Hi. I'm trying to do a sciclone-clonevol-fishplot workflow for deriving the clonal evolution of my samples. I have a case study of 4 WES samples: a primary tumor (extracted at time point 1) and three …
-
Hi,
running `deconvolve.pl` with prostate samples (benign and tumour, and cfDNA) shows no prostate in any. I also tested a tumour/normal sample from TCGA_PRAD (far right of image, prad_1, 2), which…
-
https://github.com/tgen/phoenix/blob/0e6f1e256e5f23907e81d136c0b27b1d4b2df9a5/modules/germline/main.jst#L43
After talking with Murtaza, I think to support cfDNA, and quality control efforts we shou…
-
Hi,
I tried svict on my cfDNA sample. while trying to use svict output vcf file for downstream analysis(IGV), I got this error as `Your input file has a malformed header: there are not enough colum…
-
Hi,
I have data of patient with a known microdeletion (DiGeorge). The patient is mildly affected and is pregnant and hence done NIPT for finding the chance of Digeorge in their fetus. I have the cfDN…
-
Hello,
I've been trying to get the same Canonical Transcript IDs that you uploaded in cfDNA/data/Ensembl_v75/
Though I don't come to the same list when using the above lists, to select the Canon…
-
More than an issue, this is mostly to collect some observations I made when testing (I still am) PureCN with bcbio outputs, and they may be useful for integration in bcbio.
- PureCN is *picky* on t…
-
Every overlapping read pair in HaplotypeCaller and Mutect2
goes through `FragmentUtils.adjustQualsOfOverlappingPairedFragments`, which has the following *hard-coded* logic:
```
if ( firstReadBa…
-
Hi, I have read paper of SViCT and tried to use this tool for my analysis
The compilation was successful and ran this tool using cfDNA sample and the core dump has raised.
Command line I have us…
tahuh updated
5 years ago
-
That is, multiple samples of the same tumor in space or time, a tumor and a metastasis, a tumor and its cfDNA etc.
First we have to ask collaborators and the community what features they would like…