Error asking to clean VCF, which I already did

[shafiqnoa]

I get the following error,
Please use the following command to clean your VCF file and then re-run checkVCF.py
(grep ^"#" $your_old_vcf; grep -v ^"#" $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c > $your_vcf_file

Not sure how to fix this. This code does not do anything.
I am trying to check against hg38 version. Therefore, chromosomes were coded as in hg38.fa file. I see that the same VCF file works when chromosomes were coded continuously but does not serve the purpose. Please suggest how I can solve this problem. I aim to perform imputation.

[zhanxw]

Can you give a minimal reproducible example ?

…

Sent from my iPhone

On Dec 9, 2021, at 5:18 PM, S_RAHMAN ***@***.***> wrote:  I get the following error, Please use the following command to clean your VCF file and then re-run checkVCF.py (grep ^"#" $your_old_vcf; grep -v ^"#" $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c > $your_vcf_file Not sure how to fix this. This code does not do anything. I am trying to check against hg38 version. Therefore, chromosomes were coded as in hg38.fa file. I see that the same VCF file works when chromosomes were coded continuously but does not serve the purpose. Please suggest how I can solve this problem. I aim to perform imputation. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[shafiqnoa]

A reproducible file is available in this google drive link: https://drive.google.com/file/d/1ukA9xokX6bV6cgTZOOzoAnZHoMI5A1hy/view?usp=sharing

This was my input, have not changed the header of my hg38.fa file
python heckVCF.py
-r ${REFDIR}/hg38.fa
-o test test.vcf.gz