allelic-imbalance Search Results

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weizhouUMICH/SAIGE #142

Fractional part in AC from step 2?

Dear Wei, I'm using latest version of SAIGE (0.36.3.1) for gen-based analysis: > SPAGMMATtest(vcfFile = "myvcf.vcf.gz", vcfFileIndex = "myvcf.vcf.gz.tbi", vcfField = "GT",chrom = "0", minMAF = 0…

Ojami updated 4 years ago
16
Clinical-Genomics/scout #1335

editing the panel at the gene level

I want ot change the manually curated inheritande model in a gene but it is not possible. I gent the wrong type of inheritance model type , see atttached picture ![bild](https://user-images.githubu…

4WGH updated 5 years ago
1
natsuhiko/rasqual #31

Direction of fragment count and allelic imbalance

Hello, Does RASQUAL expect that the haplotype with higher between-sample fragment count also be the haplotype with more reads in the allelic imbalance test? Thanks! Kevin

kwcurrin updated 5 years ago
6
secastel/phaser #34

Summed DNA and RNA counts in allelic_counts output file?

Dear Stephane, I used the phASER software using two input BAM files, one containing RNA-seq data, the other containing Whole Genome Sequencing DNA data. I used the --haplo_count_bam_exclude option …

freerkvandijk updated 5 years ago
5
qtltools/qtltools #15

ERROR: Unrecognized QTLtools mode!

I noticed some flags that are not described on the website when running `--help`. The names and descriptions of some of the flags imply quite interesting features that I'd like to explore if possible.…

swvanderlaan updated 5 years ago
1
natsuhiko/rasqual #32

Correlated peaks not sharing QTLs

Hi Natsuhiko, We have a very strong chromatin QTL that looks great between variant 1:109817590 and peak11858 in our data. After looking in the browser, we found three nearby peaks that are strongly…

kwcurrin updated 5 years ago
12
mskcc/tempo #137

HLA-LOH: Dockerize LOHHLA

https://www.ncbi.nlm.nih.gov/pubmed/29107330 https://bitbucket.org/mcgranahanlab/lohhla HLA LOH

evanbiederstedt updated 5 years ago
2
mskcc/facets #41

tumor-only samples or tumor with unmatched normal samples

Hi, Can facets be used for tumor-only samples or tumor with unmatched normal samples? Thanks

JoKw updated 5 years ago
11
wassermanlab/MANTA2 #1

Scores for Tissue specific ChIP Seq data

Hello, MANTA2 seems like a very convenient tool! It performed very quickly for a quick test analysis that I ran! I am interested in using MANTA2 for analyses that are mostly brain development re…

OldManTae updated 5 years ago
2
AlexsLemonade/OpenPBTA-analysis #27

Planned Analysis: Integrated CNV and SV analyses and chromot…

We have generated CNV output from [ControlFreeC](http://boevalab.com/FREEC/) and [CNVKit](https://cnvkit.readthedocs.io/en/stable/), but are seeking individuals to determine consensus focal calls and/…

jharenza updated 4 years ago
34

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87 results for allelic-imbalance

87 results
for allelic-imbalance