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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…
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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…
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I have a gVCF where the allele order of alleles not present in the genotype (`FORMAT/GT`) change when I run GATK multiple times. The resultant allele-specific values (eg. `FORMAT/PL`) all match after…
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I have a large scale dataset of WXS .g.vcfs , I do not have the original FASTA files. I would like to genotype these .g.vcfs into vcfs. These vcfs will be used in downstream applications. The issue is…
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At sometimes, the "ref" column: “the SNP-level allele-specific read counts of the reference allele” contains the float type values, for example, DNA methylation. So, is it practical to run the ASEP so…
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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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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,…
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Hi @lrauschning,
when I run `msyd call` in `--core` mode on some potato haplotypes, I get a nice PFF file of the coresyn regions and a merged VCF for the same coresyn. The SNPs and indels which do …
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Dear
I am trying to do allelic analysis Hic data getting same error G2 is mapping reads are zero and iced normalisation step getting error. I used bellow command to run analysis. non allelic analysi…
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**Is your feature request related to a problem? Please describe.**
We need consistent error codes for all errors and warnings so other tools can searh for them without error messages breaking flow.
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