Entering edit mode
5.1 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.
It worked perfectly! Thanks
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!
I have the same problem. Can you put an example of "samples.txt" please
it should just be a text file with no index or header and a single sample in each line
etc
$ bcftools query -l populations.snps_whitelistRetainedLociSamplesSingletonsHWETags.vcf | sort > sample.txt [main] Unrecognized command.
I can´t not run
Somebody can help me?
$ 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?