Loading VCF issue about radiator HOT 5 CLOSED

Hi Diede,

This is not normal behavior. Something is wrong in your VCF or strata file.

Do you mind sending the strata file: popmap_2019_LinA.tsv so that I can have a look. The VCF as well (a subset of the first few 100 lines is good enough).

If sending by email is a problem:

1. check that you have followed the instruction to generate the strata file (coming from stacks, it's really easy.

2. make sure the names are the same between the vcd and strata

Best
Thierry

from radiator.

[email protected]

from radiator.

Hi Thierry,

Whoops, sorry something went wrong with my previous comment. Anyway. I have attached a zip file with the tsv file and the first 300 lines of my vcf file.

DiedeMaas90.zip

Cheers, Diede

from radiator.

I thought the problem was fixed...
The issue, is that stacks sometimes says that the VCF contains certain info in the format field, here in the haplotype VCF:

##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

When in fact stacks just output the GT field...This is problematic for SeqArray (the VCF import engine behind radiator).

The quick fix, while I push a new version, is to keep only the GT field in the VCF header:

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

You delete those lines:

##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

This is easily done in text editor, etc.

from radiator.

I've pushed a new commit, it should work. Re-open the issue if you're still having problem.
Thanks for reporting.
Thierry

from radiator.