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genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API
MIT License
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Tumor_Seq_Allele1 and Tumor_Seq_Allele2 should be the same #268

Open leexgh opened 9 months ago

leexgh commented 9 months ago

If the variant has common postfix, e.g.

23 8993426 8993426 A CA

Problem: The current output only updates Tumor_Seq_Allele2 but fill Tumor_Seq_Allele1 with the original input

Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
23 8993425 8993426 - CA C

Expected result: Tumor_Seq_Allele1 and Tumor_Seq_Allele2 should be the same so the expected output should be:

Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
23 8993425 8993426 - C C