phase information is removed when preprocessing multiallelic sites

[hudja]

Hello,

I am unable to reopen my previous issue regarding multiallelics. So, I would make a new report.
Problem: The phase is removed when a missing ALT allele is added during the preprocessing of sites marked as multiallelic in the PharmCat VCF file.

Example input before preprocessing:

chr19	41016810	rs3211371	C	T	.	PASS	DR2=0.96;AF=0.1259;IMP;AC=1;AN=2	GT:DS:GP	1|0:1:0,1,0

After preprocessing:

chr19	41016810	rs3211371	C	A,T	.	PASS	PX=CYP2B6;AC=0,1;AN=2	GT	2/0

Pharmcat report:

{
  "gene": "CYP2B6",
  "chromosome": "chr19",
  "position": 41016810,
  "dbSnpId": "rs3211371",
  "call": "T/C",
  "alleles": [
    "*5",
    "*7",
    "*33",
    "*34"
  ],
  "phased": false,
  "phaseSet": null,
  "referenceAllele": "C",
  "hasUndocumentedVariations": false,
  "warnings": []
}

Example of detected star alleles when phase information is removed:

CYP2B6	*1/*7

and kept by manually restoring phase in the preprocessed vcf:

CYP2B6	*5/*6 OR *5/*9 OR *5/*13 OR *5/*19 OR *5/*20 OR *5/*26 OR *5/*37 OR *5/*38 OR *5/*39 OR *5/*40 OR *5/*41 OR *5/*42 OR *5/*43

Also, could you please check my reply in the other closed issue, I am not able to reopen it.

Thank you!

[markwoon]

I cannot reproduce this. I have added a basic test for this and it is passing. Feel free to modify the test so that it exhibits your issue.

Alternatively, provide me the VCF file that exhibits the issue, along with the command line you are using.

Also, could you please check my reply in the other closed issue, I am not able to reopen it.

I assume you are referring to #218. If you have a new problem, please open a new issue. If you want to continue discussing that issue, you are welcome to continue commenting in it. I see no new information in it that would warrant re-opening the issue.