I am trying to filter a bgzipped vcf file with a bgzipped bed file. I have worked a script for that using bcftools-1.9
The script is:
bcftools call -c -T bedfile.bed.gz chromosomefile.vcf.gz > filteredfile.vcf
I get an error message which says:
Wrong number of PL fields? nals=1 npl=-1
Afterwards i tried to even the script giving a .vcf.gz extention to the output file, but it retreived the same error message.
I haven't manipulated the chromosome file, nor the bed file, since i have downloaded them from a repository where they are supposed to be ready to use. I would appreciate any one of you helping to sort this problem, or suggesting any other script/tools to filter this chromosome with the bed file.
I have to say the chromosome file is a complete human chromosome, and the bed file is a list of sites which should be filtered/masked from the whole chromosome, if that info is of any use to solve the problem
Cheers everyone and thanks in advance