Story #11746

Covnert hg19 to FastJ and CGF

Added by Abram Connelly about 2 years ago. Updated 3 months ago.

Status:
New
Priority:
Normal
Assigned To:
-
Target version:
Start date:
05/24/2017
Due date:
% Done:

0%

Estimated time:
Story points:
3.0

Description

While investigating the new tile assembly construction for the "human_g1k_v37" reference, an error in the hg19 FastJ was discovered.

When converting hg19, the last tile in every path not not falling on a chromosome boundary has an extra base. Though it hasn't been confirmed, the CGF for the hg19 reference most likely also incorrectly has whatever tile variant this ending tile with the extra base has. This error was most likely introduced when initially converting the hg19 reference to FastJ by some confusion with 0 or 1 reference and whether the bounds were inclusive or exclusive from the cytogenetic boundaries.

Regenerate the FastJ for hg19, add any new tiles to the tile library and regenerate the CGF.

This most likely has minimal impact on the rest of the lightning system as hg19 is most often considered as just another genome in the pool of genome data. This might have issues for conversion back to VCF etc. though this hasn't been confirmed.

History

#1 Updated by Sarah Zaranek over 1 year ago

Abram is this finished?

#2 Updated by Jiayong Li 3 months ago

  • Target version set to Tiling 1.1

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