Hi Zihan!

• Switch to bcltools - it is faster, and (hopefully) has less bugs. bcftools

• Check sample names in your vcf files:

  for f in *.gz;do echo $f; bcftools query -l $f;done;

If you are trying to create a multisample vcf file (to merge vcf files), and you have the same sample names in different vcf files you are merging, it is a problem. Sample names should be different.

To rename a sample, you can use bcftools again:

bcftools reheader -s file_with_new_sample_names.txt vcf.gz > renamed.vcf.gz

Another way to check sample names:

gunzip -c file.vcf.gz | grep CHROM

• Remove annotations

If the source of the problem is not in identical sample names, but in the presence of annotation, then remove it before merging! The command depends on the annotator you are using. I'm using VEP which stores information in CSQ field. To remove, I'm using vt program :

vt rminfo annotated.vcf.gz -t CSQ -o naked.vcf.gz

Sergey