bcftools view -m 2 -M 2 referencePanel.vcf.gz（SV and SNP）

[SunWinner01]

Hello, sorry to bother you. Currently, I’m using the command bcftools view -m 2 -M 2 --threads 4 -Ob -o referencePanel.22.bcf referencePanel.vcf.gz to process my data. My file referencePanel.vcf.gz contains a combination of SNPs and structural variant (SV) data, with SV information included among the SNPs. However, after running this command, I noticed that there was no change in the resulting file. I’d like to ask if this is normal, as I have the following questions:

1. Does bcftools view -m 2 -M 2 have no effect on SV data?
2. What kind of SNPs would not pass the filter using the command bcftools view -m 2 -M 2?
3. In my file, the REF and ALT columns of the SNP data are composed solely of one of the letters A, G, C, or T.

These are all my questions. I look forward to your reply! Thank you so much, and I wish you all the best.

[pd3]

The command should work regardless of variant type, be it a SNP or SV. If you have a reason to suspect this is not the case and the program does something else than it should, please share a small test case to reproduce the behavior.

[SunWinner01]

example.vcf.gz
Hello, this is part of the content of my file. I hope you can use the commands I provided to process my files. I want to know why nothing changes in the result file. hope to get your reply @pd3