Tutorial:Reorder Vcf Files

Question

[chris.mit7]

Here's a quick bash script to reorder a vcf file. It's currently setup to reorder a vcf to karotypic ordering. I've seen enough threads and have been annoyed at this myself enough times so hopefully someone else finds this useful.

grep -P "^#" $1 > ${1}.header
for I in {1..22}
do
    grep -P "^$i\t" $1 > ${1}.chr$i
done
grep -P "^M\t" $1 > ${1}.chrM
grep -P "^X\t" $1 > ${1}.chrX
grep -P "^Y\t" $1 > ${1}.chrY
toCat=${1}.header
toCat="$toCat ${1}.chrM"
for I in {1..22}
do
    toCat="$toCat ${1}.chr$i"
done
toCat="$toCat ${1}.chrX"
toCat="$toCat ${1}.chrY"
cat $toCat > ${1}.karo.vcf

Usage: bash script.sh filename.vcf

It'll make a new file, filename.vcf.karo.vcf and leave the intermediates.

[lh3]

I have posted this before: alphanumeric GNU sort. It has a new option "-N" that sorts, for example, "chrM, chr10, chr2" to "chr2, chr10, chrM". For VCF sorting: (grep ^# in.vcf; grep -v ^# in.vcf|sort -k1,1N -k2,2n) > out.vcf. This works for any TAB delimited formats. It is more general, though for an already sorted VCF, it is slower.

Answer 1

[Isaac Turner]

Another solution to the problem: vcf_sort.pl

Usage: ./vcf_sort.pl <order> [in.vcf]
  Order is a comma-separated list of chroms
  Prints output to STDOUT, prints stats to STDERR

e.g.

perl vcf_sort.pl chr1,chr2A,chr2B,chr3 chimpanzee.vcf > chimp.reordered.vcf
perl vcf_sort.pl `echo chr{{1..22},X,Y,M} | tr ' ' ','` human.vcf > human.reordered.vcf

Requires the unix 'sort' command. Creates and then removes a temporary directory in the current directory.