LOH with long read data using example file provided

[rohinimopuri]

Is it possible to do LOH with the long read example data you provided. After running long_read_typing.py with the example file HG00733_pacbio.subsample.fastq.gz , there is no *freq file generated. But LOH script requires a freq file. How can I generate this?

[wshuai294]

We have not supported LOH detection based on long reads yet. However, this can be achieved intuitively. You could simply extract the genotype frequency of each heterozygous locus for each haplotype from the phased vcf, and then get the average genotype frequency for each haplotype. This will result the estimated frequency of each haplotype. After that, you could generate a freq file.