Dear all,

I have two datasets, data1 and data2, that passed the pre-imputation QC. They were all from the same original genotype data, but with different filters using plink. Data2 has more snps preserved than data1.

Now I want to check strand alignment before phasing. The command is:

shapeit -check -B data1.chr$i -M genetic_map.txt --input-ref reference.haplotypes.gz reference.legend.gz reference.sample --output-log gwas.alignment

Only difference here is the binary files ( data1.chr$i and data2.chr$i).

For data1, everything works fine. It generated .log, .snp.strand and .snp.strand.exclude files. While for data2, every chromosome works except chr13. I got .log, .snp.mm and .ind.mm files for chr13. I couldn’t figure out the reason. Anyone has an explanation?

Thanks in advance!