This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Linux command to edit CHROM column in VCF file

The contents of VCF file looks like this

I want to replace the CHROM column with chr followed by chromosome number 1 [chr1].

After using the command, the contents in the line of a VCF file should look like this

CHROM   POS    ID       REF      ALT      QUAL     FILTER     INFO     FORMAT      801   
chr1           711       .           T          C          40           PASS      DP=15     GT:GQ:DP   1|1:40:15
vcf linux
• 2,138 views • link
updated by Ram Ram • written by anilkumarboddapati • anilkumarboddapati

You can do it in R like this If you remove the headers

In Rstudio:

install.packages("dplyr")
library(dplyr)
VCF_recoded <- VCF_original %>% mutate(X.chr=recode(X.chr, 
                                                                     '1'="chr1",
                                                                     '2'="chr2",
                                                                     '3'="chr3",
                                                                     '4'="chr4",
                                                                     '5'="chr5",
                                                                     '6'="chr6",
                                                                     '7'="chr7",
                                                                     '8'="chr8",
                                                                     '9'="chr9",
                                                                     '10'="chr10", 
                                                                     '11'="chr11",
                                                                     '12'="chr12",
                                                                     '13'="chr13",
                                                                     '14'="chr14",
                                                                     '15'="chr15", 
                                                                     '16'="chr16",
                                                                     '17'="chr17",
                                                                     '18'="chr18",
                                                                     '19'="chr19", 
                                                                     '20'="chr20",
                                                                     '21'="chr21",
                                                                     '22'="chr22", 
                                                                     '23'="chrX",
                                                                     '24'="chrY"))                                 

View(VCF_recoded)
write.table(VCF_recoded,"VCF_recoded.cov", row.names=FALSE, sep=" ", quote=FALSE)

There's probs a few different ways - sorry if this isn't helpful

• 0 views • link
written by hello_bioinf • hello_bioinf

Thanks for the suggestion! I want to use the linux command for multiple files.

• 0 views • link
written by anilkumarboddapati • anilkumarboddapati

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

code_formatting

• 0 views • link
written by Ram Ram

1 answer

Has been asked before, e.g. VCF files: Change Chromosome Notation

Untested:

awk '$1 ~ /^#/ {OFS="\t"; print $0;next} {$1="chr"$1; print $0}' < in.vcf
• 0 views • link
written by ATpoint ATpoint

Thank you for the help!! It worked :). I can understand the command easily.

• 0 views • link
written by anilkumarboddapati • anilkumarboddapati

Log in to answer this question.

More posts like this