I have 7200 individual VCF files and I want to merge them into a single VCF with following command:
bcftools merge -l merge.txt -Oz -o merge.vcf.gz
What I found was if the sample counts <1021, everything is okay. However, if it is >= 1021, bcftools merge will reports:
[E::hts_idx_load3] Could not load local index file '229209.fstl1.vcf.gz.tbi' Failed to open 229209.fstl1.vcf.gz: could not load index
Does anyone know what's wrong with it?
* Problem solved, Plink doesn't have maximum limitation*
Here is bcftools version:
wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2 wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 wget https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2 wget http://s3.amazonaws.com/plink1-assets/dev/plink_linux_x86_64.zip