User: evelyn

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evelyn80
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Posts by evelyn

<prev • 151 results • page 1 of 16 • next >
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Comment: 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 evelyn80
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Comment: C: vcf file SNP position extraction
... Ultimately, I wanted the translated version of calls to do the significance test. ...
written 17 hours ago by evelyn80
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Comment: 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 evelyn80
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Comment: 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 evelyn80
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vcf file SNP position extraction
... 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 ...
snp written 1 day ago by evelyn80
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extracting one snp position from a vcd file
... Hello, Is there a way to extract one SNP by `POS` from a large vcf file. Thank you! ...
snp written 2 days ago by evelyn80 • updated 2 days ago by ATpoint30k
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Comment: C: how to remove duplicate SNP rows in vcf using bcftools norm
... Thank you! I will check again. ...
written 19 days ago by evelyn80
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Comment: C: how to remove duplicate SNP rows in vcf using bcftools norm
... @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 evelyn80
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how to remove duplicate SNP rows in vcf using bcftools norm
... 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 ...
snp written 19 days ago by evelyn80 • updated 10 days ago by Biostar ♦♦ 20
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Comment: 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 evelyn80

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Popular Question 19 days ago, created a question with more than 1,000 views. For basename: missing operand
Supporter 3 months ago, voted at least 25 times.
Centurion 4 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For C: Fastq to BAM

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