User: evelyn
evelyn • 80
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Posts by evelyn
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C: vcf file SNP position extraction
... Yes, I have REF and ALT fields. I wanted to change all the calls to R, H and A based on their respective REF and ALT fields. I tried awk but it changes to single letter REF and ALT calls only instead of R and A. Moreover, I am not sure how to deal with hetero calls.
e.g., `ch1 109 . A C A A A A A A ...
written 17 hours ago by
evelyn • 80
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C: vcf file SNP position extraction
... Ultimately, I wanted the translated version of calls to do the significance test. ...
written 17 hours ago by
evelyn • 80
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C: vcf file SNP position extraction
... I used bcftools query and it changed it to `C/C C/C C/C C/C` format. how can I change calls `0/0` to R, `0/1` to H and `1/1` to A without changing vcf file format. I did it with awk earlier but it changes the file format. ...
written 18 hours ago by
evelyn • 80
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C: vcf file SNP position extraction
... I tried to view it in Text wrangler and then copy in excel but it's still the same. I want to see if there is any significant difference between reference and alternative calls between samples for one SNP. Traditionally, I copy the SNP information in excel, convert the calls to R (0/0), A (0/1) and ...
written 1 day ago by
evelyn • 80
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... Hello,
I extracted a specific `SNP` from vcf with multiple samples using `tabix` and then I realized there are some sample names and their respective calls do not have a tab space between them and appear to be in one cell in excel. Is there a way in linux to solve this problem rather than doing it ...
written 1 day ago by
evelyn • 80
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... Hello,
Is there a way to extract one SNP by `POS` from a large vcf file.
Thank you! ...
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... Thank you! I will check again. ...
written 19 days ago by
evelyn • 80
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... @finswimmer, thank you! I have tried `D` as well but it just results in the same as input file without removing duplicates. ...
written 19 days ago by
evelyn • 80
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... Hello,
I am trying to remove duplicate SNP rows from a multiple sample vcf file. SNPs have different positions but multiple duplicate rows. I tried using
bcftools norm -d in.vcf -o out.vcf
but it does not work. Is there any other way to remove duplicates from vcf file that does not change th ...
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C: bcftools sec for multiple files
... Hello @metageni,
I have corrected the question as I have five files. I have already read the post you mentioned but I am still not sure which is the intersection file for all the combinations as the header looks the same for all output files. Thank you! ...
written 5 weeks ago by
evelyn • 80
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For basename: missing operand
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