sorting a multi-sample (genotype) vcf file

Question

[nagarsaggi]

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.

Answer 1

[finswimmer]

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

[nagarsaggi]

It worked perfectly! Thanks

[curious]

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!

[eli_ss501_midori]

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

[curious]

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

sample1
sample2
sample3

etc

[eli_ss501_midori]

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

I can´t not run

Somebody can help me?

[eli_ss501_midori]

$ 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?