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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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Hello, I believe there might be minor tweaking, but the error I am getting is
```
_scarHRD::scar_score("./seqz_inscarhrd.tsv", chr.in.names=FALSE,
+ seqz = FALSE,
+ …
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Take this segments.tsv for illustration, where both segments are > 10Mbp and display different copy number counts but same lohtype:
chr start end copy_number lohtype
1 752001 168…
ghost updated
5 years ago
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### Submitter Name
Arpad Danos
### Submitter Affiliation
Washington University
### Submitter Github Handle
arpaddanos
### Additional Submitter Details
_No response_
### Project Details
…
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Probably wrapper around https://github.com/sztup/scarHRD
lima1 updated
7 months ago
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I run scarHRD using sequenza *.small.seq.gz as input file, and I got warning message as below.
What's wrong?
> scar_score("/run/media/skanematsu/9ce21fae-49c9-4d74-a898-7ac57ac02b29/sequenza/res…
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Hi,
I have generated a allele-specific segmentation file with CNVkit. I adapted the format to fit your input
"... allele-specific segmentation file with the following columns: 1st column: sample n…
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Hello,
I was just wondering if you could take a look at whether I am correctly converting integer CNV calls from FACETS for WGS data into the correct `cnv_states` for Numbat `segs_consensus_fix`? T…
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```
a:abnormal
aMSaprakalpanA:aṃśa-kalpanā
aGnya:ághnya ({%also%} {@-yá@})
adfpita:á-dṛp-ita {%or%} {@-ta
adya:a-dyá (ā́) {%ad.%} to-day
aDarozWa,°rOzWa:adhara‡oṣṭha
aDaHsTa:adhaḥ-stha
aDipuru…
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File `hrdscore.csv` is included under DRAGEN 4.2.4 outputs. Structure is:
```
Sample,LOH_Score,TAI_Score,LST_Score,HRD_Score
FOO,9,30,20,59
```