sorting a multi-sample (genotype) vcf file
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4.5 years ago
nagarsaggi ▴ 40

I have a freebayes genotyped multisample vcf file. I want to sort the names of the samples in alphabetical order to make my life a bit easy with post variant calling analysis. I have tried Picared SortVcf which work fine which works fine on a small file but failed on a large file (~4 Gb). If you suggest ways to sort a large multi-sample file without distorting the variants information, it would a great help.

SNP • 6.0k views
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7
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4.5 years ago

Hey, try this:

$ bcftools query -l input.vcf | sort > samples.txt
$ bcftools view -S samples.txt input.vcf > output.vcf

If not already done, I would also suggest to use bcf instead of vcf or vcf.gz. This really improves speed when working with bcftools on large datasets.

fin swimmer

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It worked perfectly! Thanks

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I spent a little bit too much time trying to figure out how to do this just to come here and find this simple solution. Thanks!

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I have the same problem. Can you put an example of "samples.txt" please

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it should just be a text file with no index or header and a single sample in each line

sample1
sample2
sample3

etc

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$ bcftools query -l populations.snps_whitelistRetainedLociSamplesSingletonsHWETags.vcf | sort > sample.txt [main] Unrecognized command.

I can´t not run

Somebody can help me?

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$ bcftools query -l populations.snps_whitelistRetainedLociSamplesSingletonsHWETags.vcf | sort > sample.txt [main] Unrecognized command.

I can´t not run I send my database Somebody can help me?

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