Brandon

Thanks, Pasi. I sent an email from my gmail.

Hi Pasi, I tried this, but all outputs from SeparateChromosomes2 had all markers as singles. I tried 5704 different combinations of - xlimit : default / not specified, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 45, 60, 75, 90, 105 - lodlimit : 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98 - sizelimit...

Thanks Pasi. A couple quick questions. When you say code father as homozygote do you mean puting encoding the likelihoods as [1, 0, 0, 0, 1, 0, 0, 1, 0, 1]? with ['A/A', 'A/C', 'A/G', 'A/T', 'C/C', 'C/G', 'C/T', 'G/G', 'G/T', 'T/T'] - the mother would be all 0 By 'using' XLimit, do you mean specifying it in the command? I found some weird patters if I did not use it at all in the command. And by 'no XLimit' do you mean leaving it out of the command. I had assumed that not specifying XLimit would...

Thanks Pasi. A couple quick questions. When you say code father as homozygote do you mean puting encoding the likelihoods as [1, 0, 0, 0, 1, 0, 0, 1, 0, 1]? with ['A/A', 'A/C', 'A/G', 'A/T', 'C/C', 'C/G', 'C/T', 'G/G', 'G/T', 'T/T'] - the mother would be all 0 By 'using' XLimit, do you mean specifying it in the command? I found some weird patters if I did not use it at all in the command. And by 'no XLimit' do you mean leaving it out of the command. I had assumed that not specifying XLimit would...

Hi Pasi, 1) I'm happy to provide specific information if you'd like. The quick version is the exome capture genetic data (100 offspring per family) is from a species with haploid chromosome number of 13 (2n=26) and is output from samtools - the genome size is about 16Gbp. I have 53,000 or 81,000 SNPs depending on family (snps filtered for < 20% missing data and MAF, and informativeness like non-homozygote parental genotypes etc). I've encoded haploid genotypes as homozygous, and I also have diploid...

Hi Pasi, 1) I'm happy to provide specific information if you'd like. The quick version is the exome capture genetic data (100 offspring per family) is from a species with haploid chromosome number of 13 (2n=26) and is output from samtools - the genome size is about 16Gbp. I have 53,000 or 81,000 SNPs depending on family (snps filtered for < 20% missing data and MAF, and informativeness like non-homozygote parental genotypes etc). I've encoded haploid genotypes as homozygous, and I also have diploid...

Thanks, Pasi. I'm now on the SeparateChromosomes2 step, and neither of my families ended up with output with the correct number of linkage groups. I iterated all combinations of the following: - all possible 'informativeMask' : '0123', '1', '2', '3', '23', '13', '123' - for lodLimit - I tried all odd numbers between 0 and 50 (including 1 and 49) - sizeLimit - either 90 or 100 - all iterations I set distortionLod=1 since I have one family However as you can see with these figures, lodLimits less than...

Hi Pasi, The tissue is megagametophyte haploid tissue taken from conifer seeds with known parent(s). There was a similar dataset in the past, but maybe I misunderstood and it was an option to use XLimit=0 OR convert haplotype genotypes to homozygote genotypes - https://sourceforge.net/p/lep-map3/discussion/general/thread/525c83d8fe/?limit=25#a69c Do you think having XLimit=0 is a good choice here?