Segmentation fault in multiallelic SKAT analysis

[Tijs-dot]

Dear Zhanxw,

I tried a SKAT analysis using rvtests for a VCF file containing multiallelic variants. It seems like it almost works but fails just at the end in one of its final steps. I have provided a fragment of my VCF file and my genelist reference file (however, I also tried using the provided reference file, which gave the same error). Can you please have a look at this?

Thanks in advance,
Kind regards,
Tijs

Effective Options
--inVcf VCF_SKAT.vcf.gz
--out rvtest_skat
--covar covar_rvtest.txt
--covar-name pc1,pc2,pc3,pc4,sex
--pheno pheno_rvtest.txt
--kernel skat
--geneFile refFlat.HLA.txt.gz

connect() timeout zhanxw.com:80
Retrieve remote version failed, use '--noweb' to skip.
[INFO] Program version: 20181226
[INFO] Analysis started at: Fri Jun 4 13:06:16 2021
[INFO] Loaded [ 1349 ] samples from genotype files
[INFO] Loaded [ 1349 ] sample phenotypes
[INFO] Begin to read covariate file
[INFO] Loaded 706 male, 643 female and 0 sex-unknown samples from pheno_rvtest.txt
[INFO] Loaded 511 cases, 838 controls, and 0 missing phenotypes
[WARN] -- Enabling binary phenotype mode --
[INFO] Analysis begins with [ 1349 ] samples...
[INFO] SKAT test significance will be evaluated using 10000 permutations at alpha = 0.05 weight = Beta[beta1 = 1.00, beta2 = 25.00]
[INFO] Loaded [ 23 ] genes.
[INFO] Impute missing genotype to mean (by default)
[INFO] Analysis started
Segmentation fault

VCF format

##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FILTER=<ID=q10,Description="Quality below 10">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s1 s2 s3
6 29692078 F A ACGG,ACGA,ACGC,… . . PR GT 0/0 0/6 3/1
6 29759878 V A ACGG,ACGA . . PR GT 0/2 0/0 2/2
6 29796458 G A ACGG,ACGA,ACGC,… . . PR GT 4/6 0/0 6/6
6 29855842 H A ACGG,ACGA,ACGC,… . . PR GT 1/5 0/0 6/6

Reference file

HLA-F HLA-F-001 chr6 + 29690551 29694303 29691240 29694184 8 29690551,29691082,29691434,29691949,29692807,29693223,29693787,29694179, 29690777,29691304,29691704,29692225,29693083,29693340,29693820,29694303,
HLA-F HLA-F-004 chr6 + 29691055 29692008 29691240 29692008 3 29691055,29691434,29691949, 29691304,29691704,29692008,
HLA-V HLA-V-005 chr6 + 29758730 29760878 29760878 29760878 4 29758730,29759483,29760001,29760213, 29758763,29759551,29760082,29760878,
HLA-V HLA-V-002 chr6 + 29759682 29765588 29765588 29765588 3 29759682,29760213,29764969, 29760082,29760483,29765588,
HLA-G HLA-G-002 chr6 + 29794743 29798902 29794815 29798159 8 29794743,29795612,29795823,29796319,29797194,29797592,29798154,29798544, 29794821,29795694,29796093,29796595,29797470,29797709,29798187,29798902,
HLA-G HLA-G-201 chr6 + 29794755 29798899 29795621 29798159 8 29794755,29795509,29795823,29796319,29797194,29797592,29798154,29798544, 29794821,29795694,29796093,29796595,29797470,29797709,29798187,29798899,
HLA-H HLA-H-201 chr6 + 29855349 29857081 29857081 29857081 3 29855349,29855731,29856243, 29855607,29856001,29857081,
HLA-H HLA-H-001 chr6 + 29855528 29858259 29858259 29858259 7 29855528,29855731,29856243,29857104,29857483,29858040,29858215, 29855607,29856001,29856519,29857381,29857600,29858073,29858259,

[t0mpr1c3]

I'm getting something similar.

terminate called after throwing an instance of 'std::bad_alloc'