User: Gabriel R.
Gabriel R. • 2.5k
- Reputation:
- 2,450
- Status:
- Trusted
- Location:
- Center for Geogenetik Københavns Universitet
- Website:
- https://grenaud.github...
- Twitter:
- gabrielylr
- Scholar ID:
- Google Scholar Page
- Last seen:
- 20 hours ago
- Joined:
- 6 years, 4 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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... it depends on the aligner but it in any case, it's a bit of a scam: https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/
The link above has a plot of the distribution of mapping qualities. ...
written 8 days ago by
Gabriel R. • 2.5k
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1
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... I think this is using "samtools mpileup -s" which outputs the base quality followed by the mapping qualities for the read that supports the base. ...
written 9 days ago by
Gabriel R. • 2.5k
2
votes
1
answer
157
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1
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... These are probabilities of mismapping on a PHRED scale. For the first one, the probability of mismapping is:
(10^(-(39/10)) = 0.0001258925
For the second it is:
10^(-(50/10)) = 1e-05
So on average, your probability of mismapping is:
(0.0001258925+1e-05)/2 = 6.794627e-05
On a PHRE ...
written 9 days ago by
Gabriel R. • 2.5k
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88
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Comment:
C: TCGA SNP to plink
... Could you send a direct link to the MAF file you want to convert? ...
written 4 weeks ago by
Gabriel R. • 2.5k
0
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757
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... I just saw, this can you please provide a link to the format that you have? ...
written 8 weeks ago by
Gabriel R. • 2.5k
2
votes
1
answer
113
views
1
answers
Comment:
C: samtools and I/O redirection
... let's take a step back, why do you want a sam file to begin with? ...
written 9 weeks ago by
Gabriel R. • 2.5k
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1.0k
views
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answers
Comment:
C: Plink to Treemix
... I am not sure about your problem but you could import your plink file into [glactools][1], do the filtering and export to treemix.
[1]: https://grenaud.github.io/glactools/ ...
written 10 weeks ago by
Gabriel R. • 2.5k
0
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0
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156
views
0
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... could you post an example of the input? ...
written 11 weeks ago by
Gabriel R. • 2.5k
1
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2
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259
views
2
answers
... ok lets try the following:
1) sort your bam files wrt read names, NOT coordinates.
2) run the following:
samtools view sortedWRTnames.bam | awk '{ if(substr($1,1,1)=="@"){print $0}else{ idx=substr($1,0,12); printf("%s\t", substr($1,14)); for(i=2;i<=NF;i++){ printf("%s\t",$i); } printf("XI ...
written 12 weeks ago by
Gabriel R. • 2.5k
1
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2
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259
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2
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... yes I am aware. This is essentially a demultiplexing problem. if no one answers by the end of the day, I could be cajoled into making a slight modification to deML to account for this. ...
written 12 weeks ago by
Gabriel R. • 2.5k
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For Raxml (Residues Read In Sequence)
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For Create A Consensus Of Very Short Sequences
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For A: Evolutionary distance models
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