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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Support for Spanning or overlapping deletions #207

Closed tkmamidi closed 4 months ago

tkmamidi commented 5 months ago

Looks like the current version is ignoring star alleles. Is there a support for them in future releases? Not sure if there are databases that even support them.

SOURCE:error.converter      
LINE:5380176
INPUT:Y 56887140        .       T       *       3.52318e+06     .       AC=3280;AF=0.566;AN=5792;BaseQRankSum=0;DP=256822;ExcessHet=1074.53;FS=8.95;InbreedingCoeff=-0.3579;MLEAC=3301;MLEAF=0.57;MQRankSum=-0.445;QD=21.97;ReadPosRankSum=0.818;SOR=1.411;gnomad_hg38_af_popmax=-1;gnomad_hg38_af_afr=-1;gnomad_hg38_af_amr=-1;gnomad_hg38_af_eas=-1;gnomad_hg38_af_nfe=-1;gnomad_hg38_af_sas=-1;highest_impact_order=2147483647;gnomad_popmax_af=-1;gnomad_nhomalt=-1;gnomad_popmax_af_controls=-1;gnomad_nhomalt_controls=-1;gnomad_hg38-liftover_af_popmax=-1;gnomad_hg38-liftover_af_afr=-1;gnomad_hg38-liftover_af_amr=-1;gnomad_hg38-liftover_af_eas=-1;gnomad_hg38-liftover_af_nfe=-1;gnomad_hg38-liftover_af_sas=-1;topmed_af=-1 GT:AD:DP:GQ:PGT:PID:PL:PS       1/1:0,45:61:99:.:.:2127,175,0:.
ERROR:No valid alternate allele was found in any samples.
kmoad commented 4 months ago

We don't plan to annotate star alleles. They are mostly an artifact of large deletions and multi-sample vcfs. We are actively working on better support for annotating large deletions though.