I am attempting to combine two BCF (Binary Variant Call Format) files into a single file using the command
bcftools merge output1.bcf output2.bcf --force-samples -o test.bcf. However, when I try to view the resulting BCF file, I encounter an error message:
[W::bcf_record_check] Bad BCF record at chr01:28: Invalid INFO id 20 Error: BCF read error
To provide context, prior to merging, I filtered the BCF files using the command
bcftools filter -e 'QUAL < 30 || TYPE!="snp"' input.bcf -o output_filtered.bcf. Additionally, I indexed the filtered files using
bcftools index output_filtered.bcf.