I am attempting to phase an individual's genome using the SHAPEIT software package and am running into errors. I installed the most recent binary (r900) on a linux machine and successfully ran the software on the included example files.
I am running the program with the 1000Genomes Phase 3 reference panel that the manual recommends (link). The input file is in VCF format and was split into chromosomes using tabix. The reference genome used to generate the input file is build 38. As the reference panel is build 38, I used liftOver to lift the input VCF down to hg19/b37.
Upon running the program with the chromosome vcf, reference panel files and genetic map, the following occurs:
Segmented HAPlotype Estimation & Imputation Tool * Authors : Olivier Delaneau, Jared O'Connell, Jean-François Zagury, Jonathan Marchini * Contact : send an email to the OXSTATGEN mail list https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=OXSTATGEN * Webpage : https://mathgen.stats.ox.ac.uk/shapeit * Version : v2.r904 * Date : 02/07/2018 15:20:55 * LOGfile : [gwas.log]
MODE -phase : PHASING GENOTYPE DATA * Autosome (chr1 ... chr22) * Window-based model (SHAPEIT v2) * Reference panel of haplotypes used * MCMC iteration
Parameters : * Seed : 1530559255 * Parallelisation: 1 threads * Ref allele is NOT aligned on the reference genome * MCMC: 35 iterations [7 B + 1 runs of 8 P + 20 M] * Model: 100 states per window [100 H + 0 PM + 0 R + 0 COV ] / Windows of ~2.0 Mb / Ne = 15000
Reading unphased data in [../../genomes/chr9.vcf] Segmentation fault (core dumped)
I'm not sure how to go about fixing this. Any help is much appreciated!