Grepping samples out of vcf and writing them to a new file
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12 months ago
Kath__ ▴ 10

I am trying to select samples from a bigger vcf file and write the subset into a new vcf.gz file. The first part works well, meaning getting the samples out of the initial file. ( bcftools view initial_vcf.vcf.gz --force-samples -s samp1,samp2 )

When I try to write the new file though, I end up with a 0 bytes fcf.gz file ("unexpected end of file"). I've tried formats like this:

bcftools view initial_vcf.vcf.gz --force-samples -S selected_samples.txt | bgzip -c >  new_vcf.vcf.gz

and versions of

bcftools view initial_vcf.vcf.gz --force-samples -S selected_samples.txt -Oz -o new_vcf.vcf.gz

Any help/suggestion greatly appreciated.

VCF grep bgzip bcftools • 611 views
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is there any error message ?

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Hi Pierre, no error message, it just never finishes.

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what is the filesystem ? what is your OS ? "it just never finishes" is contradictory with " I end up with a 0 bytes fcf.gz file" ? what is the size of the initial_vcf.vcf.gz ?

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Sorry for the lack of details, I am running it on our Linux server and the original file sizes are around 70GB. And you are right, the claims are a bit contradictory, I can see a file created but nothing is written into it (thus, 0 bytes); the process never terminates though.

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the process never terminates though.

70G is high. how long did you wait ?

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Several hours, restarted a few hours ago, ps -u username shows me

02:46:37 bcftools
00:00:03 bgzip
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