User: sa9
sa9 • 800
- Reputation:
- 800
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- USA, Cambridge
- Last seen:
- 1 month, 3 weeks ago
- Joined:
- 7 years, 6 months ago
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Posts by sa9
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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
sa9 • 800
0
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254
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... Thanks Martomobo, I found a bug in my code and fixed it.
...
written 3.2 years ago by
sa9 • 800
0
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6
answers
8.3k
views
6
answers
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
sa9 • 800
1
vote
3
answers
16k
views
3
answers
Comment:
C: Pca From Vcf Files
... What is the error message? Can you post part of the VCF?
...
written 5.3 years ago by
sa9 • 800
3
votes
1
answer
2.4k
views
1
answers
... 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
sa9 • 800
1
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0
answers
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... 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
sa9 • 800
1
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4
answers
7.0k
views
4
answers
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
sa9 • 800
0
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0
answers
1.4k
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0
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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
sa9 • 800
18
votes
4
answers
7.0k
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7 follow
4
answers
... 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 ...
written 5.6 years ago by
sa9 • 800
• updated
6 weeks ago by
hugues.sicotte • 0
0
votes
0
answers
3.1k
views
0
answers
Comment:
C: Vcftools --Freq
... Could you post few lines of the input and output?
...
written 6.0 years ago by
sa9 • 800
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For Automated Plotting Of Seq. Reads In A Bam File
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For Explanation Of Heterozygous Variants Presence On Male X Chromosome (Exome Data)
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