NUlls for sample names after merging VCFs
maxineliu opened this issue · comments
Hi,
I used SURVIVOR to merge 12 single sample vcfs together.
The command I used is:
SURVIVOR merge vcf_files 1000 1 1 1 0 30 merged.vcf
The vcf_files is like:
cy201704
cy201804
cy201904
cy202304
cy202404
cy202504
cy206504
cy206604
cy206704
cy207104
cy207204
cy207304
How to fix this kind of problem? Thanks in advance!
Maxine
The vcf_files needs to hold the file names of the incividual vcf files and the paths if its run outside of the folder.
Cheers
Fritz
Hi Friz,
Sorry for I don't make it clear. The vcf_files do include the correct paths (vcfs and vcf_files sitting in one folder) and the correct names (eg. cy201704 is the name of vcf file not just the sample name. I removed .vcf from cy201704.vcf because I tried this way to avoid null name ).
Maxine
so if you do a "ls cy201704" there is a file?
Can you post the error msg and maybe a few lines before ?
I figure out why nulls happened. In each single sample vcf, the name column is filled with 'NULL'. Sorry about that!
Maxine
ah no worries :) happens
Fritz