MaryGoAround
MaryGoAround
Hello I have a list of samples from TCGA which clinical data says they have not received chemotherapy I have tried to use segmentation and marker file from firehose to...
Hello In the natural history of tumours, chromosomal arms have been intermingled and not clear like the attached plot By which argument we can make that readable please? `palimpsest_plotTumorHistories` function...
Hello I am trying to figure out how I can get the `ntot` required for clonality analysis I have `ploidy`, `purity`, `major` and `minor allele copy number` I googled for...
Sorry Is there any function in your software which extracts require fields like CHR, POST, REF, ALT, VAF, ... from a .vcf file (SNP or INDEL or SV) ? Because...
Hi I have 50 patients who have responded to chemotherapy from which 17 samples are pre-treatment biopsies and 33 patients post-treatment resections. The pre and post samples are not matched....
Hi I have 393431 SNPs, I am running `RunCcubePipeline` but likely takes indefinite time Is it possible to speed that or something a going wrong with my data?
Hi I am interested in `individual-level WGS` vcf files in `"/mnt/project/Bulk/DRAGEN WGS/Whole genome variant call files (VCFs) (DRAGEN) [500k release]"` for a list of participants in `eid.txt`. [eid.txt](https://github.com/dnanexus/UKB_RAP/files/14027174/eid.txt) I want...
I have targeted DNA sequencing for a tumour and I do not have any normal samples (matched or even non matched) I am trying this but I get error ```...
Hi I can WGS on cell lines. When I use `wgs_calling_regions.hg38.bed` as an input for making interval file and when I set `off-target regions` to `130000` for coverage calculation, I...
I have a single tumour and I done targeted DNA seq but cnvkit gets this error permanently ``` cnvkit.py heatmap converted.cns -d Traceback (most recent call last): File "/camp/apps/eb/software/cnvkit/0.9.5-foss-2016b-Python-2.7.12/bin/cnvkit.py", line...