Moderator: Matt Shirley
Matt Shirley ♦ 8.6k
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Posts by Matt Shirley
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... `faidx` was failing because the cli script expects UCSC-style regions encoded as `contig:start-end`, where `start-end` is optional. Since the HLA alt contains contain `:` characters you ran into a parsing issue. If you want to use `pyfaidx` in the same way as biopython you can do:
from pyfaidx ...
written 7 days ago by
Matt Shirley ♦ 8.6k
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Comment:
C: is this a potential mosaicism?
... It's a little more interesting to see this in blood tissue, since there's definitely more mosaicism in blood. If you have access to assays that sequence cell-free DNA, it might be interesting to see if there's an enrichment of the allele in the cfDNA, since this may be shed from some other maternal ...
written 7 weeks ago by
Matt Shirley ♦ 8.6k
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... For the mother's mosaic allele to be passed to the child you she would need to have the mosaicism present in **her** germline cells. What tissue are you sequencing? If it's a buccal sample or skin punch then it's unlikely that the same developmental progenitor cell that gave rise to the sample you s ...
written 7 weeks ago by
Matt Shirley ♦ 8.6k
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... By default the bash [read](http://tldp.org/LDP/Bash-Beginners-Guide/html/sect_08_02.html) command splits input on newline characters. So in this case `p` will be each incoming line, determined by the `\n` (newline) character. You can change the internal file separator to something like spaces or wha ...
written 9 weeks ago by
Matt Shirley ♦ 8.6k
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... You can accomplish this using `faidx -i bed genome.fa > out.bed`. For more details you can check out the documentation: https://github.com/mdshw5/pyfaidx#cli-script-faidx ...
written 10 weeks ago by
Matt Shirley ♦ 8.6k
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9.8k
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4
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Comment:
C: Converting Gvcf Files Into Vcf
... I would try Chris's suggestion, which should really be the accepted answer. ...
written 5 months ago by
Matt Shirley ♦ 8.6k
2
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... If you're going to make a script for this it's not much more effort to go all the way and do the conversion yourself:
https://gist.github.com/mdshw5/5cb686a027f805eada61b2b521ab3f13
This uses [simplesam](http://simplesam.readthedocs.io/en/latest/), which has a much simpler (get it?) API than pysam ...
written 6 months ago by
Matt Shirley ♦ 8.6k
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... What have you tried and what happened? ...
written 6 months ago by
Matt Shirley ♦ 8.6k
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... You can use `pyfaidx` for this:
pip install pyfaidx
faidx -x input.fasta
See [here](https://github.com/mdshw5/pyfaidx/blob/master/README.rst#faidx) for detailed usage. ...
written 7 months ago by
Matt Shirley ♦ 8.6k
0
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2.2k
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3
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Comment:
C: Making bed files from fasta
... I want to point out that this feature didn't work as intended until `pyfaidx` v0.5.2, where someone pointed out that the coordinate weren't 0-based half-open as expected. This has now been fixed: https://github.com/mdshw5/pyfaidx/releases/tag/v0.5.2 ...
written 8 months ago by
Matt Shirley ♦ 8.6k
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