Easy way to split VCF file by chromosome

Question

[ConvolutedGenome]

Hi,

Im trying to submit a job on the TOPMED/Michigan imputation server, but it returns an error saying that I need to split my VCF by chromosome

Is there an easy way to do this? Will bcftools help?

Answer 1

[Pierre Lindenbaum]

bcftools index -s in.vcf.gz | cut -f 1 | while read C; do bcftools view -O z -o split.${C}.vcf.gz in.vcf.gz "${C}" ; done

[ConvolutedGenome]

omg thanks!!

[rheab1230]

Hello, I tried to do this

bcftools index -s /scratch/Databases/GTEx/downloaded/dbGAP/GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz | cut -f 1 | while read C; do bcftools view -O z -o split.${C}.vcf.gz in.vcf.gz "${C}" ; done

but it throws an error:

[E::hts_open_format] Failed to open file in.vcf.gz Failed to open in.vcf.gz: No such file or directory

[Pierre Lindenbaum]

of course it doesn't work. You should have a look at my command line and _understand_ how it works.

[rheab1230]

!/bin/bash source ~/miniconda3/bin/activate conda activate train cd /scratch/downloaded/dbGAP/ for C in {1 .. 22} do bcftools index -s

in.vcf.gz | cut -f 1 | while read C; do bcftools view -O z -o /home/data_download/split.${C}.vcf.gz in.vcf.gz "${C}"; done

I tried to do this but its throwing error: line 9: syntax error: unexpected end of file