Alternative alleles not displayed correctly #533

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cmdcolin opened this Issue Nov 18, 2014 · 3 comments

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cmdcolin commented Nov 18, 2014

Previous JBrowse versions don't display the correct allele in the genotype when alternative_alleles are present.

It currently looks like this:
screenshot-localhost 2014-11-18 12-00-29

Here is how it should appear:
screenshot-localhost 2014-11-18 11-55-13

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cmdcolin Nov 18, 2014

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Here is the variant being pictured

chr 658428 . C A,T 189 . AC=2,1;AC1=1;AF=0.333,0.167;AF1=0.5;AN=6;DP=104;set=variant30-variant34-variant38 GT:GQ ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:99 ./.
./. ./. 0/2:99 ./. ./. ./. 0/1:99 ./.

Note the three variants:
0/1:99
0/1:99
0/2:99

0/1 means ref,first in the list of alternative_alleles
0/2 means ref,second in the list of alternative_alleles

and the ALT field is A,T which is the list of alternative_alleles...

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cmdcolin commented Nov 18, 2014

Here is the variant being pictured

chr 658428 . C A,T 189 . AC=2,1;AC1=1;AF=0.333,0.167;AF1=0.5;AN=6;DP=104;set=variant30-variant34-variant38 GT:GQ ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:99 ./.
./. ./. 0/2:99 ./. ./. ./. 0/1:99 ./.

Note the three variants:
0/1:99
0/1:99
0/2:99

0/1 means ref,first in the list of alternative_alleles
0/2 means ref,second in the list of alternative_alleles

and the ALT field is A,T which is the list of alternative_alleles...

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The fix was given here 1b9ff15

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cmdcolin commented Nov 18, 2014

The fix was given here 1b9ff15

@cmdcolin cmdcolin added this to the 1.11.6 milestone Jan 23, 2015

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