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Old 01-16-2013, 05:05 PM   #1
janaahan13
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Location: CA,USA

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Default Convert VCF files to BCF files

I know this question might sound stupid but is there any way we could convert vcf files to bcf files?

I created vcf files to each genome and then concatenate them to create the vcf files. I want to know is there anyways to convert it to a bcf file?
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Old 01-16-2013, 06:19 PM   #2
HerefordGuy
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Default Convert VCF files to BCF files

First off, you need to have a file with all of the chromosome identifiers. So, if you have 3 chromosomes labeled A01, A02, and A03, you need a file with this list:
Quote:
A01
A02
A03
Then you run the following command (with the appropriate file names):
Quote:
bcftools view -Sb -D chromosome.txt file.vcf > file.bcf
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Old 09-16-2015, 03:01 AM   #3
Momina
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can you tell me how to create a index of vcf file other than IGV
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Old 09-16-2015, 06:47 AM   #4
sklages
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Quote:
Originally Posted by Momina View Post
can you tell me how to create a index of vcf file other than IGV
http://lmgtfy.com/?q=how+to+create+a+index+of+vcf+file
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bcf file, bioinformatics, rna sequencing, samtools, vcf format

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