User: abascalfederico
abascalfederico • 1.1k
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Posts by abascalfederico
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... If you just want those lines with a "1" in the third column, you can add an awk command:
bcftools view -r REGION OF INTEREST | filter_vep -filter 'IMPACT is MODERATE or IMPACT is HIGH' | filter_vep -filter MAX_AF <0.01 or not MAX_AF'' | bcftools view -i 'GT="alt"' | bcftools query -f "'[%CH ...
written 3 months ago by
abascalfederico • 1.1k
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... Anyone knows of a VCF containing all human-chimp divergent sites mapped on human genome coordinates? It would be so nice if this was available :-)
Thanks!
Federico
...
written 17 months ago by
abascalfederico • 1.1k
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... For a given position, I want to read the pileup and when there is a match to the variant, I want to get the mapping coordinates of the read matching the variant. I do not have the exact code yet, but it would imply something like:
for pileupcolumn in samfile.pileup(chr,int(pos)-1,int(pos)):
...
written 3.1 years ago by
abascalfederico • 1.1k
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... Thanks, Devon. I don't want the programmatic burden ;-) I will instead make a call to python from R - not what I wanted though ...
written 3.1 years ago by
abascalfederico • 1.1k
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... Thanks Devon, I already had a look at that function, but it just provide a table of counts. I need to identify which reads support a given variant. This is relatively easy with pysam but I find no way to do this in Rsamtools. Maybe I missed something from the documentation? ...
written 3.1 years ago by
abascalfederico • 1.1k
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... For a given position, in which there is a variant called by some algorithm, I want to get the pileup and analyse the reads supporting that variant. Any idea on how to do this in R?
I know how to do this in Python using pysam but I need an R implementation.
Thanks!
...
written 3.1 years ago by
abascalfederico • 1.1k
• updated
3.1 years ago by
Devon Ryan ♦ 98k
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... Can anyone recommend a tool to segment the genome according to SNP density (using HMM-based segmentation, for example)?
Thanks!
...
written 3.4 years ago by
abascalfederico • 1.1k
• updated
16 months ago by
Biostar ♦♦ 20
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... That's exactly what I needed, thanks! ...
written 3.6 years ago by
abascalfederico • 1.1k
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... Does anybody know of a program to add the NM tag (number of mismatches) to a BAM file?
Usually aligned BAM files come with that tag, but I've found one without it and need that information.
Thanks! ...
written 3.6 years ago by
abascalfederico • 1.1k
• updated
10 weeks ago by
Biostar ♦♦ 20
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... I'll send them an email, thanks for the suggestion.
Regarding the use of bwa aln, I found it in the supplementary material of:
Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., ... & Tukiainen, T. (2016). Analysis of protein-coding genetic variation in 60,706 hu ...
written 3.7 years ago by
abascalfederico • 1.1k
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