Questions tagged [exome]
The set of all exons of a genome. Exons, as opposed to introns, are the sequences in a gene that code for a protein.
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GenomicsDB and recalibration recommended for cohort of mixed exome (GATK)
We have a cohort of around 3k exomes, most of them from different capture kits, such as Agilent v6, v8, Nextera, Twist, Clinical Research exome and many others. Right now we are creating genome db on ...
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How can I calculate the coverage of a gene in exome sequencing / calculate coverage per gene?
I have a bam file of whole exome human data. I now want to check coverage of a list of genes in my data. Basically, I want to get output like, for example:
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How to differentiate DNA fastq and RNA fastq files?
I have 2 sets of fastq files from another collaborator. The first is contains exome data and the second contains RNAseq data. But both have the RNA in the name but a different ID. How do I ...
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Manta "--exome: command not found"
I am using Manta (https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md) but whenever I try to specify the --exome command using the following code ...
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What should GC coverage bias plot of exome data look like?
I want to see if there is any GC coverage bias in some paired-end Illumina human exome data. Update This is for a variant calling project. I used the ...
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SNPs location out side the gene
I downloaded exome data from gnomad to get the allele frequency of some SNPs that I'm analyzing. The SNPs are from external resource. Some SNPs (in my data) are not present in the exome data (in ...
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Allele frequency gnomad data
I noticed that some gnomad SNPs have allele frequency =0 and some are just not found : No genes were found in this region. what is the difference between them : for example:Y-10010520-10010520.
Is all ...
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What are the columns in bedtools coverage output hist file?
I am using bedtools to caculate the coverage of my targets of my WES data, to later plot. But to plot, I need to know what to plot and what it is I am seeing. I have unsuccefully tried to find what ...
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How can I subset WGS data to the level of WES variants?
I would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome seq (i.e. ~...
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Somatic mutations for normal WES samples
I am trying to identify somatic mutations on healthy subjects (specifically in WES samples). As of now, I have found a couple of papers who have done similar studies such as this paper where somatic ...
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Non-exome variants called from whole-exome sequencing data
I'm working on rather standard whole-exome sequencing data and treat it the same as whole-genome sequencing data (aligning it to the full GRCh38 reference assembly and calling variants with no exome-...
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Calculating the number of probes for a given genomic range
I have a big data frame like this for copy number (exome seq)
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Phasing partially phased genomic data
I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array. I would like to merge the data together in the correct phase. Since ...
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Read-informed statistical phasing
I'm wondering if there are any tools out there that perform statistical phasing of genetic data (e.g. Eagle) that take read-based phasing from GATK into account. I've found this paper which sounds ...
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Why does this human bam file only have one copy of each chromosome?
As we know that in human DNA sequence, one copy of chromosome comes from mother's DNA and another copy comes from father's DNA so as to form two copies of each chromosome in human DNA. So, if we ...
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GRCm37-designed exon target enrichment, which reference to use?
I have exomes from 24 individual mice. The exomes are the product of Roche's SeqCap EZ HyperCap target enrichment kit. I see that the mouse exome design comes from mm9/NCBI37, the previous major ...
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How to get unique somatic mutations for each individual patients
I have exome data 32 patients. My aim is to identify unique somatic mutations in each patients. For this I have completed my pipeline for Whole Exome Data analysis using various tools like BWA mem, ...
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Is it possible to check if a patient has the HLA-B27 antigen from his exome stored in a VCF file
Is it possible to check if patient has the HLAB27 antigen by comparing his exome stored in VCF with all known HLAB27 variants?
For instance, rs4349859 is a known HLAB27 SNP.
If I can find rs4349859 ...
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TruSeq Exome Kit bed file old version
I have to run an analysis using Whole Exome Sequencing (WXS) data prepared with the TruSeq Exome Kit (2012).
I need the .bed file for the kit and I found it here.
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What is a good pipeline for using public domain exomes as controls?
I'm currently attempting association analysis with an extremely small set of patient exomes (n=10), with no control or parental exomes available. Downloading the ExAC VCF of variant sites (http://exac....
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Why are there missing calls in a VCF file from exome sequencing?
My data is a VCF file generated from an exome sequencing variant call pipeline. I'm not very familiar with the sequencing and variant calling process. I noticed that there are some missing genotypes, ...
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How do I validate a single sample ArrayCGH result?
We have arrayCGH (aCGH) results for one sample. There is a 0.5 Mb terminal duplication on chromosome 19 (62995490-63407936, according to NCBI36/hg18). The duplication is rare: a literature review ...
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