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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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1answer
502 views

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 ...
2
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1answer
26 views

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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1answer
105 views

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, ...
4
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1answer
116 views

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 ...
1
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1answer
71 views

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. ...
7
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1answer
135 views

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....
4
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2answers
354 views

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, ...
3
votes
1answer
42 views

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 ...