Issue in merging several vcfs

[sekhwal]

Hi, I installed bcftools and I ran bgzip and indexed the files using following commands. bgzip -c file1.vcf > file1.vcf.gz bcftools index file1.vcf.gz

However, once I merged using following command, terminal shows "killed". I have total 100 vcfs. bcftools merge ls *.vcf.gz -O v > merged.vcf

Please advise how to overcome.

[pd3]

The program seems killed by your system, possibly because of low memory. Check what version of bcftools are you using. Does it work with fewer files?

By the way, you don't have to do the `ls *vcf.gz` expansion, this can be run simply as bcftools merge *.vcf.gz. Unless you are using some obscure shell, that is.

[sekhwal]

Yes! it works with 5 or less than 5 vcfs. However, once I do with more than 9 vcfs. The process is Killed.

I created an conda environment and I installed bcftools using the command: conda install bcftools. if I use bcftools --version, it shows:

bcftools 1.11 Using htslib 1.11 Copyright (C) 2020 Genome Research Ltd.

[valeriuo]

What does the kernel log show you? Run cat /var/log/kern.log, if you have permission, or dmesg -k just after bcftools is killed.