search

WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
234 stars 359 forks source link

Truncated VCF output at chr21 #242

Closed snakesch closed 7 months ago

snakesch commented 7 months ago

Dear Dr Wang,

Thank you for the amazing tool!

I was using this tool to annotate a pool of variants called by GATK using WGS data. When I tried to use gnomad v4 frequency data and a reference assembly with chrM and all the alternative contigs, the output VCF only writes variants til chr21. Nothing from chr22 onwards were written. May I know if you have encountered a similar issue while working with gnomad v4? If necessary, I will try to work on a minimally reproducible example VCF, but this should take some time as patient genotype data might not be shared.

Look forward to your expert advice and suggestion.

Thanks and regards, Louis

kaichop commented 7 months ago

This could be due to many reasons including out of memory and disk I/O issue. You can split the input VCF into several parts and the combine final results together. Also check the intermediate files which may have all results written since the last step of handling VCF file is to convert a tab-delimited text file to VCF.

On Fri, Apr 12, 2024 at 7:43 AM Louis @.***> wrote:

Dear Dr Wang,

Thank you for the amazing tool!

I was using this tool to annotate a pool of variants called by GATK using WGS data. When I tried to use gnomad v4 frequency data and a reference assembly with chrM and all the alternative contigs, the output VCF only writes variants til chr21. Nothing from chr22 onwards were written. May I know if you have encountered a similar issue while working with gnomad v4? If necessary, I will try to work on a minimally reproducible example VCF, but this should take some time as patient genotype data might not be shared.

Look forward to your expert advice and suggestion.

Thanks and regards, Louis

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/242, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OEOCX37546VWKZWR7LY47CGHAVCNFSM6AAAAABGD7UATWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTSOJVGM4DMOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

snakesch commented 7 months ago

Dear Dr Wang,

Thank you for the advice. I just found an I/O issue with the variant calling step where a significant portion of variants was discarded. The issue has nothing to do with gnomad 4.0 and other annotation resources.

Sorry for the oversight and I shall close this issue.

Regards, Louis