I am having an issue when trying to perform bcftools merge. I get these errors with the first file in the list,
[E::hts_hopen] Failed to open file filename1.bcf.csi [E::hts_open_format] Failed to open file filename1.bcf.csi Failed to open filename1.bcf.csi Exec format error
I take .bcf files and index them with
bcftools index ... using
htsfile I find my files are indeed "CSI version 1 compressed index data", of "BCF version 2.2 compressed variant calling data", originally from files of "VCF file version 4.2 variant calling text" I am using "BCFtools Version: 1.9 (using htslib 1.9)"
this is my script:
bcftools merge --missing-to-ref --file-list /vol_c/scripts/file_list.txt --merge all --threads 14 --output all58_samples.vcf