Variant Annotation Integrator - phyloP100 issue

[Paolo Uva]

Dear UCSC staff,

I'm encountering a a problem with Variant Annotation Integrator.

I uploaded successfully as a custom track a VCF with 7,000 lines,
with variants sorted as chr1...chr9,chr10...chr22, chrX, chrY.

I submit to VAI, selecting just '100 vertebrates Basewise Conservation
by PhyloP'.
In the "Select Genes" section, I selected 'UCSC genes' (default).

VAI runs and produces a file with variants from chr1 to chr9 only.
The last line contains the following message:
'Unsorted input from primary source (chr10 < chr9)'

...but my input VCF is sorted as chr1...chr9,chr10...chr22, chrX, chrY.

If I split the original VCF in two parts:
-part1: chr1 to chr9
-part2: chr10 to 22, X, and Y
the two output files are correct.

Thanks,

Paolo

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Paolo Uva
CRS4 Bioinformatica
Loc. Piscina Manna
09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it

[Steve Heitner]

Hello, Paolo.

This is the result of the way the VAI is specifically expecting the file to be sorted. Currently, it expects to see:

chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
chrY

We will work on relaxing the sorting expectations, but in the meantime, you can sort your VCF file with the following and try again:

sort -k1,1 -k 2n,2n my.vcf > my.ucsc.vcf

Please contact us again at gen...@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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