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atks / vt

A tool set for short variant discovery in genetic sequence data.
http://genome.sph.umich.edu/wiki/vt
MIT License
190 stars 3 forks source link

Decomposition of multi-allellic loci lose Number=G type INFO fields #87

Closed mmoisse closed 6 years ago

mmoisse commented 6 years ago

I noticed that when you decompose multi-allellic variants the lose all INFO fields of type Number=G

##INFO=<ID=GC_Male,Number=G,Type=Integer,Description="Count of Male individuals for each genotype">
wget https://storage.googleapis.com/gnomad-public/release/2.0.2/vcf/genomes/gnomad.genomes.r2.0.2.sites.chr15.vcf.bgz.tbi
wget https://storage.googleapis.com/gnomad-public/release/2.0.2/vcf/genomes/gnomad.genomes.r2.0.2.sites.chr15.vcf.bgz
tabix -h gnomad.genomes.r2.0.2.sites.chr15.vcf.bgz 15:72639383-72639383  | grep GC_Male
tabix -h gnomad.genomes.r2.0.2.sites.chr15.vcf.bgz 15:72639383-72639383 | ~/software/vt/current/vt decompose -s - 2>/dev/null | grep GC_Male
atks commented 6 years ago

@mmoisse - I can't download the file by wget, what do you use in this case for google storage?

The issue is not due to authentication but rather the resource appears to be missing.

mmoisse commented 6 years ago

It was the wrong URL I updated it now.

atks commented 6 years ago

@mmoisse - it used to work correctly, I haven't touched this code for a long time so it might be due to changes in htslib. This might take a bit of time to fix.

atks commented 6 years ago

@mmoisse - could you pull it and check it, it was actually a bug that had never been fixed.

mmoisse commented 6 years ago

@atks it works like it should now! Thank you for the quick fix!