VCF to BCF file conversion

Question

[SOHAIL]

Hi Everyone,

I am sorry this might be stupid, but can anyone help me, is there any way:

1. To convert VCF file to BCF file. I think we can use BCFTOOLS but I am not getting the right command.
2. My VCF file has soe duplicated records, how to filter the duplicate records of variants?

Thanks in advance!

[Pierre Lindenbaum]

I think we can use BCFTOOLS but I am not getting the right command.

What did you try?

[SOHAIL]

I tried bcftools

bcftools view file.vcf.gz -o file.bcf

Answer 1

[Pierre Lindenbaum]

in the manual: https://samtools.github.io/bcftools/bcftools.html#view

-O, --output-type b|u|z|v Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when piping between bcftools subcommands to speed up performance by removing unecessary compression/decompression and VCF←→BCF conversion.

[SOHAIL]

Thank you very much for your comment Pierre, can you please guide me how I can generate .BCI file for BCF (*..bcf.bci), I am trying to call de novo mutations by de novo gear software and I need this input file.

But by BCFtools, we can only generate CSI index file (https://samtools.github.io/bcftools/bcftools.html#index)

and can you please comment on how to remove duplicate records fro VCF file?

Thanks!