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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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Extracted .vcf file has empty ”.” in REF and QUAL columns #134

Open Albert-Stefansen opened 2 years ago

Albert-Stefansen commented 2 years ago

Hello, we are trying out CNVpytor v.1.2.1 for possible inclusion in our snakemake pipeline in which we would import the read depth, predict CNV regions and output as .vcf format for use in programs as IGV or VarSeq.

However, the output vcf file has empty columns (marked as ".") for the REF (reference bases) and QUAL (quality). When checking the applied reference genome using:

cnvpytor -root file.pytor -ls

The correct hg19 genome is shown, but the output .vcf file shows:

reference=GRCh37

In the third line. All other columns of the vcf. file seem to be correct expect the reference and quality. Does anyone know what may be causing the problem? Our workflow consists of the generic -rd, -his, -partition and -call commands followed by extraction of the .vcf file by using the CNVpytor viewer.

Thanks in advance. Kind regards Albert Stefansen

krukanna commented 1 year ago

Hi, I got the same - empty REF and QUAL. Is it possible for CNVpytor to complete this information? The most important for me is the QUAL column. Thanks

ramprasadn commented 1 year ago

I am also facing the same issue so I just wanted to add that some functionalities in Picard/bcftools (maybe most or all, I am not sure) don't work because they expect the REF column to have a valid entry.

Albert-Stefansen commented 1 year ago

Thanks for expressing your encounter of this problem too. I hope that someone from the dev team will reply soon with a solution to this issue.

ramprasadn commented 1 year ago

@arpanda any idea how to workaround this issue? We are currently using cnvnator and we really like cnvpytor. However, we are not able to make the switch as it doesn't work well with the rest of our pipeline because of this specific issue 😅

arpanda commented 1 year ago

Pytor file doesn't store the reference sequences and an additional parameter probably needed to add the REF in the VCF output. I will check the possibility of it.

Could you give an example of the commands you are trying to use from bcftools and Picard. I will try to reproduce the error.

-Arijit

arpanda commented 1 year ago

I have updated the code that creates the vcf file and REF column is still empty. One possible easy solution is to add N instead of . Could you please use the latest cnvpytor and try the bcftools/Picard and share the error.

Command to install latest version of CNVpytor

pip install git+https://github.com/abyzovlab/CNVpytor.git

-Arijit