Function mismatch for CYP2D6 *1 > Normal Function != null while running analysis

[NTNguyen13]

• Do you want to request a feature or report a bug? I want to report a bug

• What is the current behavior? Error Function mismatch for CYP2D6 *1 > Normal Function != null while running analysis Full Error log

  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
  >>> WARNING: This is pre-release software, not for production use <<<
  >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
  org.pharmgkb.pharmcat.UnexpectedStateException: Function mismatch for CYP2D6 *1 > Normal Function != null
      at org.pharmgkb.pharmcat.definition.PhenotypeMap.lambda$new$0(PhenotypeMap.java:50)
      at java.util.ArrayList.forEach(ArrayList.java:1251)
      at org.pharmgkb.pharmcat.definition.PhenotypeMap.<init>(PhenotypeMap.java:37)
      at org.pharmgkb.pharmcat.reporter.ReportContext.<init>(ReportContext.java:64)
      at org.pharmgkb.pharmcat.reporter.Reporter.analyze(Reporter.java:140)
      at org.pharmgkb.pharmcat.PharmCAT.execute(PharmCAT.java:164)
      at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:86)

• If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar. I used multiple variant callers to call the variants on a WGS sample, with respect to a PGx bed files. Then I run pharmcat and encounter this problem on all vcf from different callers (HaplotypeCaller, VarDict, FreeBayes, DeepVariant)

What have gone wrong in my case? Thank you

• Please tell us about your environment:

  • PharmCAT Version: 0.7.0
  • JDK Version: OpenJDK 1.8
  • Environment: Ubuntu 16.04

[NTNguyen13]

dive a bit deeper, when I remove the chr22 from my bed file, it works. I test the same bed file against NA12878 sample aligned by NYGC, it works. The only different is that my bam file is aligned without ALT-handling while the NA12878 has it.

[NTNguyen13]

I found 2 variants causing the problem: chr22 42126611 . C G 510.64 . AC=1;AF=0.5;AN=2;BaseQRankSum=1.59;DP=37;ExcessHet=3.0103;FS=1.271;MLEAC=1;MLEAF=0.5;MQ=59.57;MQRankSum=-1.603;QD=14.18;ReadPosRankSum=0.123;SOR=0.465 GT:AD:DP:GQ:PL 0/1:21,15:37:99:518,0,723 chr22 42130692 . G A 1203.64 . AC=1;AF=0.5;AN=2;BaseQRankSum=1.64;DP=49;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=26.75;ReadPosRankSum=1.15;SOR=0.749 GT:AD:DP:GQ:PL 0/1:12,33:47:99:1211,0,332

[definitivequestion]

I get a similar error as given below: org.pharmgkb.pharmcat.UnexpectedStateException: Function mismatch for CYP2D6 *10 > Decreased Function != null at org.pharmgkb.pharmcat.definition.PhenotypeMap.lambda$new$0(PhenotypeMap.java:50) at java.util.ArrayList.forEach(ArrayList.java:1251) at org.pharmgkb.pharmcat.definition.PhenotypeMap.(PhenotypeMap.java:37) at org.pharmgkb.pharmcat.reporter.ReportContext.(ReportContext.java:64) at org.pharmgkb.pharmcat.reporter.Reporter.analyze(Reporter.java:140) at org.pharmgkb.pharmcat.PharmCAT.execute(PharmCAT.java:164) at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:86)

[tizatt]

I also got a similar error. This was using a DeepVariant vcf :

org.pharmgkb.pharmcat.UnexpectedStateException: Function mismatch for CYP2D6 *3 > No Function != null
    at org.pharmgkb.pharmcat.definition.PhenotypeMap.lambda$new$0(PhenotypeMap.java:50)
    at java.util.ArrayList.forEach(ArrayList.java:1257)
    at org.pharmgkb.pharmcat.definition.PhenotypeMap.<init>(PhenotypeMap.java:37)
    at org.pharmgkb.pharmcat.reporter.ReportContext.<init>(ReportContext.java:64)
    at org.pharmgkb.pharmcat.reporter.Reporter.analyze(Reporter.java:140)
    at org.pharmgkb.pharmcat.PharmCAT.execute(PharmCAT.java:164)
    at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:86)

[whaleyr]

The PhenotypeMap data has changed since v0.7 and Sep 2020. Is this still an issue when using v0.8 or the current main branch?

I'm assuming this has been fixed. I'll keep this open for a while but I'll close it if I don't hear anything in a while.

[markwoon]

Please try again with the latest version. If this is still a problem, please open a new issue.