I am having difficulty running SHAPEIT for my specific case - I am getting
Segmentation fault. Nothing that I managed to find online solved my problem.
In principle, I want to phase a subset of SNPs present in two, separated regions of the X chromosome, for a single sample. I am using a .vcf file as input.
The command I would typically run would be:
shapeit --input-vcf Mix0_1_S1/RD_RHDA_v1_1/data/full_variant_table.vcf \ -M genetic_map_chrX_nonPAR_combined_b37.txt \ --output-log Mix0_1_S1.chrX.log \ --output-max Mix0_1_S1.tab \ --chrX \ --input-ref 1000GP_Phase3_chrX_NONPAR.hap.gz 1000GP_Phase3_chrX_NONPAR.legend.gz 1000GP_Phase3.sample \
I also tried various other options (restricting to a smaller region, changing window size, not using reference etc) but no matter what I do I get the enigmatic
Segmentation fault message just when reading the .vcf. I would appreciate any help.
PS. I am running v2.r904