User: sa9

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sa9800
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USA, Cambridge
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Posts by sa9

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Indel Left/Right Alignment
... Thanks Erik. Vt is awesome. We have been using it for couple of months now. ...
written 3.0 years ago by sa9800
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Comment: C: simulating samtools -f option in pysam
... Thanks Martomobo, I found a bug in my code and fixed it. ...
written 3.2 years ago by sa9800
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Comment: C: Rare Variant Association Analysis
... A more recent (2014) review  for any one interested in this topic http://www.cell.com/ajhg/abstract/S0002-9297%2814%2900271-7 ...
written 4.3 years ago by sa9800
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Comment: C: Pca From Vcf Files
... What is the error message? Can you post part of the VCF? ...
written 5.3 years ago by sa9800
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Comment: C: Why Does A Query For Single Position Yield Neighboring Positions In Tabix?
... Please try not to use words like "major bug" in the title unless you are 100% sure. It is very irritating, especially when you use floats for genomic coordinates. ...
written 5.5 years ago by sa9800
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Comment: C: I16 Tag In Vcf File - Samtools Mpileup
... using "bcftools view" without option outputs I16 values as in: samtools mpileup -gDSf g1k_v37.fasta file.bam | bcftools view - but you don't get the I16 if you add arguments to the "bcftools view" (e.g -gcv) , AFAIK. ...
written 5.5 years ago by sa9800
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Comment: C: Indel Left/Right Alignment
... Thanks Ixe, we used similar tool from GATK specifically for VCF files (http://goo.gl/0f7bT) but as lh3 pointed out, it is too late to correct in the VCF file. ...
written 5.5 years ago by sa9800
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Comment: C: Error In Running Denovogear
... hmm you posted another question http://www.biostars.org/p/67563/#67591 and both are short on details. Please give some information on what did you do so far (input files, command used, arguments etc) so someone can help you. ...
written 5.6 years ago by sa9800
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Indel Left/Right Alignment
... When matching indels between different VCF files (generated by different callers), there is this issue with left / right indel alignment, For example: Here is a real example for one indel (from the same sample) called by: Samtools --> 1 161047125 CTATA C GATK --> 1 ...
indel written 5.6 years ago by sa9800 • updated 6 weeks ago by hugues.sicotte0
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Comment: C: Vcftools --Freq
... Could you post few lines of the input and output? ...
written 6.0 years ago by sa9800

Latest awards to sa9

Guru 10 months ago, received more than 100 upvotes.
Epic Question 13 months ago, created a question with more than 10,000 views. For Math Guide For Bioinformatics
Great Question 15 months ago, created a question with more than 5,000 views. For Automated Plotting Of Seq. Reads In A Bam File
Great Question 20 months ago, created a question with more than 5,000 views. For Automated Plotting Of Seq. Reads In A Bam File
Great Question 21 months ago, created a question with more than 5,000 views. For Automated Plotting Of Seq. Reads In A Bam File
Good Question 21 months ago, asked a question that was upvoted at least 5 times. For Automated Plotting Of Seq. Reads In A Bam File
Good Question 24 months ago, asked a question that was upvoted at least 5 times. For Math Guide For Bioinformatics
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Pca From Vcf Files
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Pca From Vcf Files
Great Question 3.6 years ago, created a question with more than 5,000 views. For Math Guide For Bioinformatics
Good Answer 4.1 years ago, created an answer that was upvoted at least 5 times. For A: Pca From Vcf Files
Good Question 4.1 years ago, asked a question that was upvoted at least 5 times. For Math Guide For Bioinformatics
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Explanation Of Heterozygous Variants Presence On Male X Chromosome (Exome Data)
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Explanation Of Heterozygous Variants Presence On Male X Chromosome (Exome Data)
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Math Guide For Bioinformatics
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Pca From Vcf Files
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Pca From Vcf Files
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Rare Variant Association Analysis
Appreciated 4.5 years ago, created a post with more than 5 votes. For Math Guide For Bioinformatics
Appreciated 4.5 years ago, created a post with more than 5 votes. For Automated Plotting Of Seq. Reads In A Bam File
Librarian 4.5 years ago, created a post with more than 10 bookmarks. For Math Guide For Bioinformatics
Good Question 4.5 years ago, asked a question that was upvoted at least 5 times. For Math Guide For Bioinformatics
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Math Guide For Bioinformatics
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Automated Plotting Of Seq. Reads In A Bam File

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