User: felipead66
felipead66 • 30
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Posts by felipead66
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... I have a multi-sample vcf file annotated with snpeff.
I want to calculate the linkage disequilibrium.
I have 2 questions:
1. I use vcftools, in particular `./vcftools --vcf input_vcf.vcf --geno-r2 --out output` and it takes forever (it runs a week and keeps on). Is this OK?
2. Is it appropria ...
written 10 weeks ago by
felipead66 • 30
• updated
10 weeks ago by
RamRS ♦ 23k
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... Is it possible to extract the fasta sequences of specific genes from a snpeff output (vcf) file?
...
written 12 weeks ago by
felipead66 • 30
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Comment:
C: Chromosomal length prunus dulcis
... Thank you for your reply,
I followed the instructions in the link and I would not trust it since I get around 10000 (!) chromosomes. So there must be something else, I do not know what went wrong. ...
written 12 weeks ago by
felipead66 • 30
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... Is it possible to find the chromosomal length of prunus dulcis?
https://www.rosaceae.org/organism/Prunus/dulcis
I want to use it to build circus plots. ...
written 12 weeks ago by
felipead66 • 30
• updated
12 weeks ago by
SMK • 1.8k
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... Thank you very much, that is every helpful.
But, still, how do I get the non_synonymous?
Furthermore, I assume that the synonymous_variant are in the coding region? ...
written 3 months ago by
felipead66 • 30
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... You mean the command line to create the snpEffoutput.vcf file? ...
written 3 months ago by
felipead66 • 30
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... Yes, this gives me 81949 results.
But again, when I do
`grep -c 'non_synonymous' snpEffoutput.vcf I` still get 0 results. ...
written 3 months ago by
felipead66 • 30
• updated
3 months ago by
finswimmer ♦ 12k
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... I have a vcf file after using snpEff annotation.
I want to extract information from this file so I search for synonymous (and non-synonymous) sites.
But when I do
grep -c "SYNONYMOUS" snpEffoutput.vcf
I get 0 results.
Does this mean there is something wrong with my file? ...
written 3 months ago by
felipead66 • 30
• updated
3 months ago by
finswimmer ♦ 12k
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... typo, the correct is "snp identification" ...
written 3 months ago by
felipead66 • 30
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... I have read some papers that use plink in their studies for snps. I also have read plinks' documentation.
I have not, though, figured out WHEN to use the plink in the process for snp identification.
Could you please give some advice on when to use plink? ...
written 3 months ago by
felipead66 • 30
• updated
3 months ago by
WouterDeCoster ♦ 40k
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