User: hamid.khape

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Posts by hamid.khape

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Comment: C: How can I be sure that the mpileup result is correct, and what is the reasons f
... I mean the expected output. I mean how I can make sure that some thing is not wrong with the mpileup output. After the mpileup command, I am doing some analyses with VarScan. Unfortunately, the output is not what it should be. Therefore, I want to know what could be wrong here. By the way, I am u ...
written 8 months ago by hamid.khape0
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Comment: C: De novo mutation definition
... Is there any text book explaining de-novo mutation? I want to refer to it. Thank you ...
written 8 months ago by hamid.khape0
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Comment: C: Trio data base for de-novo mutations
... Yes, I have access, but I do not want to generate those files by my self. In addition, some BAM or FASTQ files of the samples are missing in the data part, so it is better to find a new data base. There is no final goal. It is a class assignment. ...
written 8 months ago by hamid.khape0
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Trio data base for de-novo mutations
... I am new in bioinformatics. I am looking for a database containing **healthy** trios VCF files so that I can find de-novo mutations of a child in a family. I have tried 1000 genome project, but most of the children are missing in the phase 3 VCF files. ...
genome alignment snp written 8 months ago by hamid.khape0
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Comment: C: De novo mutation definition
... I have counted the number of mutation in a number of trios. For example, the sample X has 760 de novo mutations based on what we discussed. In the VCF file, the FILTER part of most of the positions is PASS. What could be wrong? I have checked the code, and everything is OK! The samples are healthy, ...
written 8 months ago by hamid.khape0
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Comment: C: De novo mutation definition
... Thank you for your comment. Regarding the VCF file, what should I do? There are a lot of mutations that have been reported in the file and could be de novo, but this is not right because de novo must be rare. The file does not have any QUAL part so that I can filter the calls. ...
written 8 months ago by hamid.khape0
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Comment: C: De novo mutation definition
... The QUAL column is ".", so there is no information. No I have not produced the VCF file. It is a VCF file from 1000 genome project data set. Here is the link: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip/ALL.chip.omni_broad_sanger_combined.20140818.snps.geno ...
written 8 months ago by hamid.khape0
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Comment: C: De novo mutation definition
... Thanks for your answer. Well, this was just an example to explain what is my problem. Actually, in a VCF file, I am looking for de novo mutation in a particular family, and I have counted 760 mutations that was seen in child, and it was not inherited from parents just like the above-mentioned examp ...
written 8 months ago by hamid.khape0
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De novo mutation definition
... I'm new in bioinformatics. I'm looking for an exact definition of de novo mutation in trios. I've read this definition, but it's not including what I'm looking for (or I didn't understand it). " A genetic alteration that is present for the first time in one family member as a result of a variant (or ...
snp written 8 months ago by hamid.khape0 • updated 8 months ago by Kevin Blighe51k

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