Adjust selscan.py to correctly read allosomal VCF files.
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tomkinsc commented
Within cms/tools/selscan.py, alter process_vcf_into_selscan_tped() so it will correctly act on allosomal VCF files. Of note is that within the genotypes for chromosome X, some sample records will be singletons (i.e. men, ex. "0"), while some will be phased pairs (i.e. women, ex. "0|1"). This will require adjusting the creation of the index list used to access the genotypes by position, or creating an alternate, slower, code path that is more flexible.