User: Yahan

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Yahan370
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370
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Belgium
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7 months ago
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8 years, 2 months ago
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Posts by Yahan

<prev • 21 results • page 1 of 3 • next >
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Comment: C: can discoSnp make the distinction between homeologous loci
... Thanks for the clear explanation Pierre. ...
written 9 months ago by Yahan370
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can discoSnp make the distinction between homeologous loci
... In polyploid genomes with limited variation between subgenomes generally read mapping is a challenge leading to frequent read mismapping and hence calling homeologous variants, eg variations that are actually differences between the subgenomes. When using discoSnp, you can imagine that these loci c ...
discosnp homeologous loci snp written 9 months ago by Yahan370 • updated 9 months ago by pierre.peterlongo830
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Comment: C: Guessing The Quality Scale In Fastq Files
... link is meanwhile broken also. ...
written 12 months ago by Yahan370
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Comment: C: Combining Data Of Multiple Vcfs Into One.
... Hi Malachi, How will joinx behave when score annotation is absent for reference calls? I have a rather large bunch of VCF files with calls for all positions (gVCF?) but the annotation is different between positions with and without a call GT:DP versus GT:AD:DP:GQ:PL I tried with the lastest versio ...
written 2.9 years ago by Yahan370
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Comment: C: Combining Data Of Multiple Vcfs Into One.
... link is dead... ...
written 2.9 years ago by Yahan370
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query PL field with bcftools
... Hi BioStars, I'd like to find the highest PL value (posterior likelihood for each possible genotype) for each sample in my VCf file. From the documentation, I know that you can do  MAX(DP) which will find you the highest genotype depth over all samples Since the PL field has a value for each p ...
bcftools view snp query written 3.2 years ago by Yahan370
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Answer: A: Which Bioinformatic Friendly Pipeline Building Framework?
... Bpipe is the tool of choice here. Excellent support for threading, easy restarting of jobs that failed at certain step in the workflow, easy stitching together different steps, management of input and output naming. https://code.google.com/p/bpipe/ Amazing it's not in here already ...
written 3.7 years ago by Yahan370
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Answer: A: Variant Analysis on MiSeq Data
... Assuming that you are working in a grid environment, what we use is bpipe, an excellent tool to develop pipelines and workflows. You could use it to perform the different steps needed to arrive at your snp calling. One of the advantages of bpipe is that it manages the parallelisation of the differen ...
written 3.7 years ago by Yahan370
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Comment: C: snp calling using reference with no raw data
... Well, we want to know the genotype call for the raw-less sample(s), provided that the calls from the other samples are confident enough to accept the snp. We will then filter downstream for assay design taking the calls for all samples into account. So I would maybe not use the raw-less calls for qu ...
written 4.0 years ago by Yahan370
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snp calling using reference with no raw data
... I have to do a snp calling on 40 or so samples a few of which originate from public sources. For these the raw data is not available in all cases. Therefore I thought of building a dummy fastq paired dataset by chopping the reference into pieces using a window approach to add some coverage. Any th ...
snp calling written 4.0 years ago by Yahan370 • updated 4.0 years ago by geek_y8.8k

Latest awards to Yahan

Great Question 9 months ago, created a question with more than 5,000 views. For Gene Expression In Rnaseq Data
Popular Question 19 months ago, created a question with more than 1,000 views. For Formatdb And Non Coding Characters
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Extracting Sequence From A 3Gb Fasta File
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Create Image From Mapping Region
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Extracting Sequence From A 3Gb Fasta File
Appreciated 4.7 years ago, created a post with more than 5 votes. For A: Extracting Sequence From A 3Gb Fasta File
Good Answer 4.7 years ago, created an answer that was upvoted at least 5 times. For A: Extracting Sequence From A 3Gb Fasta File
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Gene Expression In Rnaseq Data
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Extracting Sequence From A 3Gb Fasta File
Student 4.7 years ago, asked a question with at least 3 up-votes. For Gene Expression In Rnaseq Data
Student 4.7 years ago, asked a question with at least 3 up-votes. For Formatdb And Non Coding Characters

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