-
Hi there,
since GDC release 23 there is a new readout for TCGA, 'Allele-specific Copy Number Segment'. It would be great if it were downloadable in TCGAbiolinks via:
```R
query.cnv = TCGAbiolin…
-
Hello Nicholas
Firstly thanks for developing this tool, it's really helpful!
Now I have Hi-C data from one individual, and I want to compare the contacts between two alleles (to see if allelic heter…
-
Consider using the individual, sample, metadata, and variant core APIs as templates for a genotype + phenotype query language.
For example, we can ask for information about alleles in a specific coho…
-
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…
-
Hi Weilong,
I am trying to analyze allele specific methylation and while performing analysis using below parameter
$ cgmaptools asm -r refgenome.fa -b sample1_sorted.bam -l sample1_bayes.vcf -o s…
-
Writing some test cases for symbolic allele parsing, I've encountered some problems with the SV specifications when dealing with multiple SV alt alleles since only some fields support multiple alleles…
-
The VCF spec discusses symbolic alleles as `an angle-bracketed ID String “”` (in 1.6.1.4) but the overlapping deletion allele is `*`. I suspect that the intention is that the star allele be considered…
-
Hello Sir/Ma'am,
A very convincing normalisation approach well explained in the paper.
So we have the allele specific read count from Single-cell RNA seq data without a…
-
During the Kinship Matrix section, there was discussion about using allele probabilities vs genotype probabilities. There was a specific question about why you would choose to use one over the other,…
-
Add an option to filter by position or for specific variants instead of gene name; check the reference allele for input variants.