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Questions - bcftools

Extract variant positions from VCF dependent on contents of other columns

I have a vcf file, I am trying to extract the information from these columns: #CHROM POS REF ALT However I would like to extract these only if the SAMPLE-1 column contains the string DeNovo (N...
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hdjc90

awk

sed

samtools

vcftools

bcftools

Votes: 0

Answers: 1

Latest Answer

FWIW, I'm not familiar with bcftools but if the intention is to pipe the bcftools output into awk then we could do the whole thing in awk ... Assumptions: none of the fields (in the file) contain whi...
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markp-fuso

Replace 2nd and 3rd occurrence of a character with another character, for each line, Bash

I am trying to reformat the reference legend files to make them compatible with bcftools. Essentially, I need to go from this: id position a0 a1 TYPE AFR AMR EAS EUR SAS ALL 1:123:A:T 123 A T SNP 0.01...
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FranjoIM

bash

bioinformatics

bcftools

Votes: 0

Answers: 1

Latest Answer

If sed is an option: sed 's/:/_/2; s/:/_/2' file > reformatted_file (This command s/:/_/2 is substituting the second ":" to an underscore, then substituting the third ":" to an...
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jared_mamrot

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