Efficient Way to Split Huge VCF Files by Chromosome | Inquiry

Question

[S]

Hello, I have been spending significant time trying to split a large VCF file into its individual chromosome files.

Here is the code I have been using (it works, but in a very inefficeint manner):

for i in {1..22}; do vcftools --chr chr$i --gzvcf "$(input_vcf)" --recode --recode-INFO-all --out "$(output_name-chr-$i); done 

In my trials I have considered a few options:

1. The implementation of tabix to index the large multi-chromosome vcf and then its subsequent incorporation into this code.
2. BCFtools view command

I feel that the answer lies in the realm of BGZIP and Tabix, although I am still stuck. I also am unsure exactly how tabix and bgzipping helps in the processing of high-throughput data, I would greatly appreciate any help.

I appreciate your time and consideration.

Thank you

[Jeremy Leipzig]

what is your end goal?

[S]

The end goal is to go from a large multi-chromosome vcf file (around 600 GB) and output 22 single chromosome vcf files. Then these will be run through a pipeline that is able to process the separate pieces (the software I am using cannot run through the large file). Thank you

Answer 1

[GenoMax]

Please use answers in this thread : Easy way to split VCF file by chromosome