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=

FILTER=

FORMAT=

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,

zhanxw / rvtests

Segmentation fault in multiallelic SKAT analysis #123