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WansonChoi / CookHLA

An accurate and efficient HLA imputation method.
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Producing input files for MakeGeneticMap #6

Closed juliandwillett closed 2 years ago

juliandwillett commented 2 years ago

I am having difficulty in preparing the input files for this function. Given that I am starting with CRAM files, I convert to BAM and then to BED using samtools and bedtools. I then sort the bed files. I am having difficulty merging these bed files as the code and examples seem to suggest as I need to do. I was wondering if anyone has a solution to this (I have tried using cat to join them all and then using mergeBed, but I was told there was an out of order record with the start coordinate being outside of the region I specified [28999852 when specified the start coordinate as 29000000])

juliandwillett commented 2 years ago

Overcame issue by merging VCF files and then using Plink on this.