User: Gabriel R.
Gabriel R. • 2.5k
- Reputation:
- 2,490
- Status:
- Trusted
- Location:
- Center for Geogenetik Københavns Universitet
- Website:
- https://grenaud.github...
- Twitter:
- gabrielylr
- Scholar ID:
- Google Scholar Page
- Last seen:
- 22 hours ago
- Joined:
- 6 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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Comment:
C: reference genome hs37d5 with PhiX
... I am no longer there, I will ask my former supervisor, let's see if they can stick it somewhere. in the meantime, here are the accessions for the reference: http://cdna.eva.mpg.de/neandertal/Chagyrskaya/bam/README
...
written 19 days ago by
Gabriel R. • 2.5k
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Comment:
C: reference genome hs37d5 with PhiX
... perhaps I am wrong but there is no "the reference with PhiX". When I was at the Max Planck Inst. in Leipzig, we made our own by concatenating the human reference and some decoy sequences. I suggest you contact the center in question that produced the BAM file. ...
written 19 days ago by
Gabriel R. • 2.5k
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Answer:
A: deML 'rgqual' parameter
... The rgqual refers to the Z_0 score. Z_0 is the likelihood for the top (most likely) read group on a PHRED scale. Considering the sequence of this read group as the template to sequence and using the principle of independence between bases, this likelihood is computed as:
Z_0= -10 * log_10{ PROD ...
written 25 days ago by
Gabriel R. • 2.5k
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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 10 weeks ago by
Gabriel R. • 2.5k
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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 10 weeks ago by
Gabriel R. • 2.5k
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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 10 weeks ago by
Gabriel R. • 2.5k
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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 3 months ago by
Gabriel R. • 2.5k
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... I just saw, this can you please provide a link to the format that you have? ...
written 4 months ago by
Gabriel R. • 2.5k
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150
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Comment:
C: samtools and I/O redirection
... let's take a step back, why do you want a sam file to begin with? ...
written 4 months ago by
Gabriel R. • 2.5k
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1.1k
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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 4 months ago by
Gabriel R. • 2.5k
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