What are the best resources or tools to sort an unsorted human gVCF

Question

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I'm trying to process a gVCF file "genome882131.hard-filtered.gvcf" and I haven't previously seen the 'hard-filtered.gvcf" extension. I simply changed the .gvcf extension to .vcf to process it.

I encountered an issue using tabix on this file, however, as the data appears to be unsorted. When I tried to run tabix, the following errors were returned:

[E::hts_idx_push] unsorted positions
tbx_index_build failed: /mnt/data/workDir/225121/genome8821.hard-filtered.vcf
Could not load .tbi index of /mnt/data/workDir/225121/genome8821.hard-filtered.vcf

I checked Bcftools but it doesn't provide sorting functionality. Are there resources or tools that will sort this unsorted vcf so that it will work with tabix?

[John]

tabix really should have told you why it thinks it's unsorted. If you think about it, it's actually kind of funny that it gives an error that simply says "unsorted". That's really about as useful as saying "this data has gone off." or something. Then you have to Google what fresh data should look like. derp.

You probably need a unix sort command for gVCF, but i'm not confident what the sorting requirements are for tabix, particularly for chromosomes, so I don't want to suggest something that's wrong :(

Answer 1

[ssv.bio]

did you try igvtools in sorting gVCF?