I wanted to merge vcf files using
bcftools merge --file-list sample_list.txt -O v -o merge.vcf
But it gives an error for sample16.vcf.gz
Error: Duplicate sample names (sample16.vcf.gz), use --force-samples to proceed anyway.
Although I do not have any other vcf file with the same name in the same directory. I still used,
bcftools merge --force-samples -m none --file-list sample_list.txt -O v -o merge1.vcf
Now it gives a weird name to that particular sample in the output file:
I am not sure if it is extracting right information from sample16.vcf file or not. I compared this file column from merged file with individual vcf file and it is not same.
I will appreciate any help to figure out this problem of duplicate names of files. Thank you!