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.

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[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