An error is thrown, despite all chromosome names and rs being coherent:
Using user-specified VCF file to calculate LD with reference SNP chr8:1234..
Error: while calculating LD from VCF file: index SNP position 1234 does not exist in file..
First of all I did not understand, so I modified vcf_ld.py to be more explicit by printing the tabixed region, the error was:
Error: while calculating LD from VCF file: tabix returned null for region 8:1234-1234.
This fails because the chromosomes in the VCF are prefixed by 'chr', as in, chr8.
It would be useful to add smart handling of "chr" prefixes.
While running the following command:
An error is thrown, despite all chromosome names and rs being coherent:
First of all I did not understand, so I modified
vcf_ld.py
to be more explicit by printing the tabixed region, the error was:This fails because the chromosomes in the VCF are prefixed by 'chr', as in,
chr8
.It would be useful to add smart handling of "chr" prefixes.