User: Stephwen

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Stephwen140
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Bioinformatician

Posts by Stephwen

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Computing B-Allele Frequency From Bam Or Vcf Related To Exome Samples
... Thanks for the thorough answer! ...
written 7.1 years ago by Stephwen140
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Computing B-Allele Frequency From Bam Or Vcf Related To Exome Samples
... Hi everyone, I would like to compute BAF profiles for samples whose exome has been sequenced. I thus have the BAM files, and VCF files containing the SNPs, which were called with a GATK-based pipeline. At first I thought about using the VCF files, and considering that each position which is not pr ...
vcf exome frequency allele bam written 7.1 years ago by Stephwen140 • updated 7.1 years ago by Irsan7.1k
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Answer: A: Cytogenic Location To Genome Coordinates In R
... You could also directly download the coordinates of the cytoBands: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz ...
written 7.4 years ago by Stephwen140
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Comment: C: Polymorphic Genes And Filtration In Exome Sequencing
... Very interesting idea. I have personally come across MUC4, KIR3DL1, and HYDIN as candidates in a family exome study recently. They weren't ruled out as potential candidates when I did an effect prediction with SIFT and PolyPhen. Such a list could be very helpful to help further filter candidate gen ...
written 7.5 years ago by Stephwen140
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Answer: A: Incorrect Reference Base In 'Samtools Mpileup' Output
... Perhaps we could further complete the information present in this table : http://alternateallele.blogspot.de/2012/03/genome-coordinate-cheat-sheet.html and save it on some wiki somewhere (seqanswers?), as this kind of question seems to arise periodically. ...
written 7.8 years ago by Stephwen140
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Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?
... Hello everyone, I'm currently using GASV ( http://code.google.com/p/gasv/ ) to find structural variants in human whole genome data. To filter out variants which I consider irrelevant, I want to filter out variants situated in highly repetitive regions such as centromeres and telomeres and also oth ...
genome repeats database human written 8.5 years ago by Stephwen140 • updated 16 months ago by Charles Warden7.6k

Latest awards to Stephwen

Appreciated 6.5 years ago, created a post with more than 5 votes. For Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?
Great Question 6.5 years ago, created a question with more than 5,000 views. For Computing B-Allele Frequency From Bam Or Vcf Related To Exome Samples
Great Question 6.5 years ago, created a question with more than 5,000 views. For Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?
Good Question 6.5 years ago, asked a question that was upvoted at least 5 times. For Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?
Popular Question 6.5 years ago, created a question with more than 1,000 views. For Computing B-Allele Frequency From Bam Or Vcf Related To Exome Samples
Popular Question 6.5 years ago, created a question with more than 1,000 views. For Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?
Supporter 6.5 years ago, voted at least 25 times.
Student 6.5 years ago, asked a question with at least 3 up-votes. For Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?

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