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Converting Thousand genome BCF file into VCF with BCFtools

Hi All.

I am trying to convert 1000 Genome BCF files into VCF files using bcftools and process is getting quit automatically after just converting 2-3 chromosomes. Just wondering if some one else is getting same problem as well ?

bcftools view ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.bcf | bgzip -c > ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.vcf.gz

If problem is due to bgzip or bcftools ?

This one is version of BCFtools that I am using. bcftools 1.3 Using htslib 1.3

bcftools
• 5,730 views • link
updated by Jorge Amigo Jorge Amigo • written by always_learning always_learning

Is there an error message? How large is your bcf?

• 1 views • link
written by dschika dschika

1 answer

instead of piping the output to bgzip, try creating the output file directly:

bcftools view -Oz \
-o ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.vcf.gz \
ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.bcf

you do know you have the latest .vcf files already available, don't you?

• 1 views • link
written by Jorge Amigo Jorge Amigo

Yes I know but since I had .bcf file already to trying to convert that only. Thanks

• 1 views • link
written by always_learning always_learning

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