Question: VCF to BCF file conversion
1
gravatar for SOHAIL
3.3 years ago by
SOHAIL220
Beijing Institute of Genomics, CAS.
SOHAIL220 wrote:

Hi Everyone,

I am sorry this ight 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!.

 

genomics ngs analysis • 6.0k views
ADD COMMENTlink modified 3.3 years ago by Pierre Lindenbaum114k • written 3.3 years ago by SOHAIL220

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

what did you try ?

ADD REPLYlink written 3.3 years ago by Pierre Lindenbaum114k

I tried bcftools 

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

ADD REPLYlink written 3.3 years ago by SOHAIL220
2
gravatar for Pierre Lindenbaum
3.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k wrote:

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

 

-O, --output-type b|u|z|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.

ADD COMMENTlink written 3.3 years ago by Pierre Lindenbaum114k

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 tryinh to call de novo utations 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! 

 

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by SOHAIL220
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