From ff31f83cfe54ad1d76a3bfa775adcb2ccc9d0d80 Mon Sep 17 00:00:00 2001 From: Ivo Fokkema Date: Fri, 29 May 2020 14:15:06 +0200 Subject: [PATCH] Silently skip variants that currently don't have a supported mapping to a transcript. - If variants partially map outside of a transcript, VV currently does not return a transcript mapping, but also no liftover. As such, we can do nothing. - See https://github.com/openvar/variantValidator/issues/173. - Silently skipping these variants for now. --- src/scripts/fix_variant_descriptions.php | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/scripts/fix_variant_descriptions.php b/src/scripts/fix_variant_descriptions.php index 451e5650..8986d334 100644 --- a/src/scripts/fix_variant_descriptions.php +++ b/src/scripts/fix_variant_descriptions.php @@ -577,6 +577,16 @@ function ($sVOT) && count($aVV['data']['genomic_mappings']['hg38']) == 1) { // We have a hg38 DNA column, and this variant has only one hg38 mapping. $aVV['data']['DNA38_clean'] = substr(strstr($aVV['data']['genomic_mappings']['hg38'][0], ':'), 1); + } elseif (empty($aVV['data']['genomic_mappings']['hg38']) + && empty($aVV['data']['transcript_mappings']) + && empty($aUpdate)) { + // Variant has no hg38 mapping, no liftover, and we have nothing to update. + // Probably the mapping isn't supported, because the variant partially lies outside of the transcript. + // On 2020-05-29, that's still a known problem, and probably will be for a while. + // https://github.com/openvar/variantValidator/issues/173 + // We've decided, for now, to skip these variants. + $this->nProgressCount ++; // To show progress. + continue; // Then continue to the next variant. } else { $this->panic($aVariant, $aVV, 'None or multiple hg38 mappings given for variant.'); }