User: Rob

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Rob90
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2 years, 9 months ago
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Posts by Rob

<prev • 36 results • page 1 of 4 • next >
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Wrong genotype assignation in GATK?
... Hello, I am looking at some GATK VCF results, and I found something I can't explain. There is this result for one of my SNP: GT:AB:AD:DP:GQ:MQ0:PL 0/1:1.00:21,0:22:79:0:79,0,708 The concerned field is the AD which is the "*Allelic depths for the ref and alt alleles in the order listed*". ...
vcf gatk genotype snp written 5 months ago by Rob90
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Comment: C: Software for Tree Visualization
... No other software since 6.3 years? ...
written 17 months ago by Rob90
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Comment: C: De novo pacBio genome assembly: How to polish data without quiver?
... Well, I use Canu alone, and it don't contain a polisher. I wll try to use the pacBio polisher. ...
written 19 months ago by Rob90
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De novo pacBio genome assembly: How to polish data without quiver?
... I am currently working on some de novo genome assembly with pacBio data. I used Canu for assembly but I didn't have access to quiver (or arrow) for data polishing. What can I do now? I can't find any tools for replace quiver, so I'm a little bit stuck... Thanks ! ...
quiver sequencing polishing pacbio assembly written 19 months ago by Rob90 • updated 19 months ago by Alex20
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... Yep, only one sample (same RG tag for each Lane) ...
written 20 months ago by Rob90
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... The strange things with this is that I have more coverage on a single SNPs without merge the files before. Here one example (same for all SNPs common in both methods) : Ref Alt QUAL GT DP Without merge: T C 48.0158 0/1 26 With merge ...
written 20 months ago by Rob90
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... But since the RG tags are identical for one sample, doesn't mpileup merge files itself? And so the coverage should be identical compared to the step with merge no? ...
written 20 months ago by Rob90
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... I will try more research, because yeah, that is the information I'm looking for :) So which way do you personally suggest as the best? Merge first sample with same RG tags, and do variant calling on the merged file? ...
written 20 months ago by Rob90
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... But what mpileup do with the 2 files informations? Since it's the same sample (with identical @RG tag), does not it merge them together too? ...
written 20 months ago by Rob90
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Comment: C: how to parse blast output using biopython
... I think you are 2 years late.. And everything about biopython is writen [here][1] [1]: http://biopython.org/DIST/docs/tutorial/Tutorial.html ...
written 20 months ago by Rob90

Latest awards to Rob

Popular Question 5 months ago, created a question with more than 1,000 views. For Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple BAM
Voter 17 months ago, voted more than 100 times.
Popular Question 24 months ago, created a question with more than 1,000 views. For How to properly merge multiple runs into one bam file ?
Supporter 2.2 years ago, voted at least 25 times.

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