We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Hi, I encountered an error as follow: Files:
GLIMPSE_split_reference parameters:
Splitting reference panel:
Parsing specified genomic regions
and here is my command: REF=filled_10xquchong.bcf while IFS="" read -r LINE || [ -n "$LINE" ]; do printf -v ID "%02d" $(echo $LINE | cut -d" " -f1) IRG=$(echo $LINE | cut -d" " -f3) ORG=$(echo $LINE | cut -d" " -f4) GLIMPSE2_split_reference --reference ${REF} --input-region ${IRG} --output-region ${ORG} --keep-monomorphic-ref-sites --output 10x.chr1 done < chunks.chr1.txt
I tried both bcftools norm -f and bcftools +fill-tags,but not work ,the error remains. Would appreciate any suggestions, or ideas, thanks!
The text was updated successfully, but these errors were encountered:
No branches or pull requests
Hi, I encountered an error as follow:
Files:
GLIMPSE_split_reference parameters:
Splitting reference panel:
Parsing specified genomic regions
�[31mERROR: �[0mAC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF
and here is my command:
REF=filled_10xquchong.bcf
while IFS="" read -r LINE || [ -n "$LINE" ];
do
printf -v ID "%02d" $(echo $LINE | cut -d" " -f1)
IRG=$(echo $LINE | cut -d" " -f3)
ORG=$(echo $LINE | cut -d" " -f4)
GLIMPSE2_split_reference --reference ${REF} --input-region ${IRG} --output-region ${ORG} --keep-monomorphic-ref-sites --output 10x.chr1
done < chunks.chr1.txt
I tried both bcftools norm -f and bcftools +fill-tags,but not work ,the error remains.
Would appreciate any suggestions, or ideas, thanks!
The text was updated successfully, but these errors were encountered: