User: Gabriel R.
Gabriel R. • 2.6k
- Reputation:
- 2,590
- Status:
- Trusted
- Location:
- Center for Geogenetik Københavns Universitet
- Website:
- https://grenaud.github...
- Twitter:
- gabrielylr
- Scholar ID:
- Google Scholar Page
- Last seen:
- 4 hours ago
- Joined:
- 7 years, 6 months ago
- Email:
- m***************@yahoo.com
Now postdoc at the Center for Geogenetics at Copenhagen University. In a former life, I was a Ph.D student in bioinformatics at the Max Planck Institute for Evolutionary Anthropology/ Interested in sequencing, particularly ancient DNA and inference of demography.
Posts by Gabriel R.
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... Could you post a few sequences and a mini diagram of what you expect like [Adapter] [UMI] [SEQ] .. ? ...
written 25 days ago by
Gabriel R. • 2.6k
1
vote
1
answer
90
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Comment:
C: Merging unaligned bam files
... What is wrong with samtools cat? ...
written 4 weeks ago by
Gabriel R. • 2.6k
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2
answers
160
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Answer:
A: Allele count from BAM file
... It is one line in [glactools][1]:
glactools bam2acf [reference].fa [iinput].bam sampleid | glactools view - |cut -f 1-3,6
In the last column, the format is REF,ALT:cpg
Be aware that it filters out reads marked as QC failed and PCR duplicates.
[1]: https://grenaud.github.io/glactools/ ...
written 8 weeks ago by
Gabriel R. • 2.6k
1
vote
1
answer
280
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1
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... You can try [glactools][1], it is just one line:
glactools vcfm2acf --onlyGT --fai /Data/reference/human_g1k_v37.fasta.fai /tmp/biostars/test.vcf | glactools acf2bplink - /tmp/biostars/test
You need to edit the genetic distance in the bim file and probably the fam files as well.
[1]: h ...
written 3 months ago by
Gabriel R. • 2.6k
0
votes
2
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195
views
2
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... But there are many different haplotypes in India. What do you mean Indian origin? ...
written 3 months ago by
Gabriel R. • 2.6k
0
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1
answer
390
views
1
answers
... if you have dedicate cycles, it's ok, I was wondering about the output format. ...
written 4 months ago by
Gabriel R. • 2.6k
0
votes
1
answer
390
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1
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... I don't get it. You will simply prime next to read2 and hope to run into the barcode+UMI? ...
written 4 months ago by
Gabriel R. • 2.6k
0
votes
1
answer
390
views
1
answers
... But that is assuming the adapters were sequenced. Were there sequencing cycles to sequence the indices? ...
written 4 months ago by
Gabriel R. • 2.6k
0
votes
1
answer
390
views
1
answers
... Could you post a few lines as example? Do you have an index list? ...
written 4 months ago by
Gabriel R. • 2.6k
0
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0
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210
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0
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... I am not 100% sure but ANGSD only implements the error model in GATK with "-gl 2" and the samtools one with "-gl 1" ...
written 4 months ago by
Gabriel R. • 2.6k
Latest awards to Gabriel R.
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Merge Scaffolds From Different Individuals?
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Good Answer
11 months ago,
created an answer that was upvoted at least 5 times.
For A: What Skills Do You Have To Have As A Phd Graduate In Bioinformatics?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Psmc Parameters To Use
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Great Question
12 months ago,
created a question with more than 5,000 views.
For Out Of Disk Space With Picard Tools ?
Scholar
14 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Scholar
18 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Raxml (Residues Read In Sequence)
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Create A Consensus Of Very Short Sequences
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Scholar
23 months ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: How To Interpret The Kmer Enrichment Plot Of A Fastqc Output
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Evolutionary distance models
Good Answer
2.1 years ago,
created an answer that was upvoted at least 5 times.
For A: What Software Programs Do Bioinformaticians Need?
Student
2.2 years ago,
asked a question with at least 3 up-votes.
For Out Of Disk Space With Picard Tools ?
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Merge Scaffolds From Different Individuals?
Epic Question
2.4 years ago,
created a question with more than 10,000 views.
For Out Of Disk Space With Picard Tools ?
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