README_9_merge_vcf_files.md

Merge VCF files

The horizontal combination through BCFTools merge consists in combining multiple VCF files containing the same information about different samples (i.e., there is no overlap between sample IDs in all of the VCF files). Thus, the merge command can be used to obtain a single VCF file with the merged samples from the query and the reference.

It is the user's responsibility to ensure that the sample names are consistent across all files. Unless the option —-force-samples is specified, the application will exit with an error. It is worth noting that only records from different files can be merged, never from the same file. Look into BCFtools concat for vertical merging.

Usage

To use merge from bcftools:

bgzip -ci <query_allchr.vcf> > <query_allchr.vcf.gz>
bgzip -ci <reference_allchr.vcf> > <reference_allchr.vcf.gz>

rm -f file.list
for F in <query_allchr.vcf>.gz <reference_allchr.vcf.gz>
do
      bcftools sort -O b -o ${F}.bcf $F
      bcftools index ${F}.bcf
      echo "${F}.bcf" >> file.list
done

bcftools merge --file-list file.list -O z -o <merged_file>

For more information, read the documentation.

Example

bgzip -ci query_allchr.vcf > query_allchr.vcf.gz
bgzip -ci reference_allchr.vcf > reference_allchr.vcf.gz

rm -f file.list
for F in query_allchr.vcf.gz reference_allchr.vcf.gz
do
      bcftools sort -O b -o ${F}.bcf $F
      bcftools index ${F}.bcf
      echo "${F}.bcf" >> file.list
done

bcftools merge --file-list file.list -O z -o merged.vcf.gz