jltsiren
commented
2 days ago We have never tried the method with read coverage lower than 20x.
With 10x read coverage, kmer coverage will likely be 7x or 8x. Kmers that occur 2-5 times will be classified heterozygous and those that occur 6-17 or 6-20 times homozygous. The classification will be noisy, but I can't say in advance if it will be good enough.
Hi, When haplotype sampling based on kmer counts in the reads, the Note told that read coverage should be at least 20x to tell the difference between heterozygous and homozygous kmers reliably. The read coverage of my data is about 10x, so could I still use this method? Thank you!