[ensembl-dev] dev-owner at ensembl.org
helens at ebi.ac.uk
Thu Jun 13 09:05:37 BST 2019
On 07/06/2019 18:44, David Tamborero wrote:
> Hi Helen
> FYI, if I m not wrong at this time of the day, VEP run (--tab output)
> stops(w/o any msg or warning file created) as soon as a line
> with REF==ALT is reached, so it does not seem to need to 'accumulate'
> a number of these 'non-variant' entries
I am looking into this. Is the variant following the line with REF==ALT
on the same chromosome?
> on the other hand, as you say, when using vcf as output with the
> --allow_non_variant flag, entries as e.g.
> 12 111352091 16500 C C . PASS
> are included in the output w/o any annotation,
When using VCF format as input and output, by default VEP will skip
non-variant lines of input (where the ALT allele is null).
Enabling the --allow_non_variant option the lines will be printed in the
VCF output with no consequence data added.
VEP expects the ALT allele to be null to skip non-variant lines e.g.
#CHROM POS ID REF ALT QUAL FILTER INFO
22 17181903 var_1 A G . . .
22 17188416 var_2 T . . . .
22 19353405 var_3 G A . . .
> and have a nice weekedn
> El vie., 7 jun. 2019 a las 18:25, Helen Schuilenburg
> (<helens at ebi.ac.uk <mailto:helens at ebi.ac.uk>>) escribió:
> Hi David
> Thanks for the information.
> The VEP should skip non-variant lines of input by default and not
> We will look at updating the stats to report the lines skiped.
> When using VCF format as input and output, by default VEP will
> skip non-variant lines of input. Please could you try running
> your sample variants with vcf output (--vcf) and --allow_non_variant.
> With the text output, it should also skip the non-variant lines.
> VEP could be stopping on your input file, if it has skipped a
> number of non-variant lines. We will look into this
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