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### Need
As a clinical geneticist, I need an improved CNV workflow for targeted panel sequencing (UMI & non-UMI), in particular for cfDNA samples, to accurately detect genetic variations.
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Hi @colindaven @sannareddyk @B1T0 @Colorstorm @BioNij
Wochenende ran well when we inputed cfdna fastq profiles containing human reads as well with other pathogenic reads.
We were interested in…
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In addition to cfDNA, whether the ichorCNA can be used for gDNA？
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Hi, it seems `numpy` does not have `float` anymore (now it's included in `base`). I had a problem running:
```
$ svviz2 --ref ~/references/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.modifi…
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Hello,
For some data sets, I occasionally met error error "unrecognized CIGAR operator" when run gemBS map.
The debug imformation is as follows:
Bisulfite Mapping...
2019-11-14 10:16:56,579 D…
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Currently, I have been using ichorCNA for cfDNA analysis in HCC. However, results of several patients showed that their tumor fraction equal to 0. Is there a theoretical threshold for ichorCNA detecti…
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Hello,
I have used the following config file:
```
[general]
chrLenFile = /media/prodriguez/disk1/Databases/genomes/Hsapiens/hg19/seq/chromosomes/hg19.fa.fai
window = 0
ploidy = 2,3
outputDi…
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Lims Issue
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For definitions of headings below see [Basic Concepts](https://atlas.scilifelab.se/infrastructure/lims/basic_concepts/).
**Work Flow:** TWIST v8
**Protocol:** Pre Processi…
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Command executed:
bcftools annotate --header-lines /Data/data/raja/cfdna/nextflow1/bin/syn3_header.txt LCR_FILTERED > FILTERED_hd.vcf
**java -jar -Xmx4g /Data/data/raja/cfdna/nextflow1/bin/snp…
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I'm looking at the new cfDNA methylation document put out by ONT https://community.nanoporetech.com/knowledge/know-how/cfDNA-methyl-profile and it has some figures on % methylation by read position.
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