Dear all,
I am trying to use the Sanger imputation service (https://imputation.sanger.ac.uk/), but I get the following error:
"Reference allele mismatch at 1:752566 .. REF_SEQ:'G' vs VCF:'A'"
According to this link https://imputation.sanger.ac.uk/?resources=1, this can be fixed by installing bcftools and using the fixref plugin available here https://github.com/pd3/bcftools/blob...ugins/fixref.c
However, after installing bcftools, there are no plugins:
I have downloaded fixref.c and placed it in /usr/local/libexec/bcftools but still nok luck. If I try to compile fixref.c I get:
Despite bcftools being installed:
Not really sure what to do here?
I am trying to use the Sanger imputation service (https://imputation.sanger.ac.uk/), but I get the following error:
"Reference allele mismatch at 1:752566 .. REF_SEQ:'G' vs VCF:'A'"
According to this link https://imputation.sanger.ac.uk/?resources=1, this can be fixed by installing bcftools and using the fixref plugin available here https://github.com/pd3/bcftools/blob...ugins/fixref.c
However, after installing bcftools, there are no plugins:
Code:
bcftools plugin -vl plugin directory /usr/local/libexec/bcftools .. ok No functional bcftools plugins were found. The environment variable BCFTOOLS_PLUGINS is not set.
Code:
gcc fixref.c fixref.c:84:22: fatal error: bcftools.h: No such file or directory #include "bcftools.h" ^ compilation terminated.
Code:
which bcftools /usr/local/bin/bcftools
Comment