Eric Gonzalez

Many thanks Pasi, I’m sorry, I’m not entirely sure how to use the FindContigErrors flag. These are the options I can see: java -cp bin FindContigErrors usage: java FindContigErrors [options] chain=file chain file paf=file load alignment file in paf (minimap2) format proximity=file NUM1 NUM2 NUM3 load proximity data, NUM1=bin size [10000] NUM2=max distance in bins [25], NUM3=scale score [1.0] I think I can generate the chain file using the steps described here: https://sourceforge.net/p/lep-anchor/wiki/Home/#creating-alignment-chains-for-haplotype-removal...

Thank you very much, Pasi. I’m finally getting back to this project. I used the FitStepFunction, but I noticed that it is not working as I expected. For example, I’m attaching one chromosome that I believe shows a very clear inversion. Before and after applying FitStepFunction, it’s evident that the function just removes the linkage information inside the inversion. For large, clear inversions like this one, I could flip them manually, but for smaller ones it might be harder to detect. So, I’d like...

Many thanks for your answer. I would like to use use the FitStepFunction from Lep-Rec. I am trying to do this: java -cp /LEP-REC/bin FitStepFunction map=order_LG1_informativeMask1_reevaluated.mapped But I am getting this error: java FitStepFunction map=order_LG1_informativeMask1_reevaluated.mapped java.lang.NumberFormatException: For input string: "0.000" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67) at java.base/java.lang.Integer.parseInt(Integer.java:668)...

Many thanks for your answer. I would like to use use the FitStepFunction from Lep-Rec. I am trying to do this: java -cp /LEP-REC/bin FitStepFunction map=order_LG1_informativeMask1_reevaluated.mapped But I am getting this error: java FitStepFunction map=order_LG1_informativeMask1_reevaluated.mapped java.lang.NumberFormatException: For input string: "0.000" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67) at java.base/java.lang.Integer.parseInt(Integer.java:668)...

Many thanks for your answer. I would like to use use the FitStepFunction from Lep-Rec. I am trying to do this: java -cp /LEP-REC/bin FitStepFunction map=order_LG1_informativeMask1_reevaluated.mapped But I am getting this error: java FitStepFunction map=order_LG1_informativeMask1_reevaluated.mapped java.lang.NumberFormatException: For input string: "0.000" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67) at java.base/java.lang.Integer.parseInt(Integer.java:668)...

Thank you very much for your response. My maps are still a bit messy. I used your pipeline to obtain the genotype likelihoods (GL) for Lep-MAP3 with Samtools: samtools mpileup -q 10 -Q10 -s $(cat sorted_bams)|java Pileup2Likelihoods [options] >post.txt Since I didn’t apply any of the usual filters I use for SNP calling, I think I need to add some filtering to improve my plots. I’m considering adding a read depth filter. Pileup2Likelihoods already has a minimum read depth filter of 3 reads, which...

Thank you very much for your response. My maps are still a bit messy. I used your pipeline to obtain the genotype likelihoods (GL) for Lep-MAP3 with Samtools: samtools mpileup -q 10 -Q10 -s $(cat sorted_bams)|java Pileup2Likelihoods [options] >post.txt Since I didn’t apply any of the usual filters I use for SNP calling, I think I need to add some filtering to improve my plots. I’m considering adding a read depth filter. Pileup2Likelihoods already has a minimum read depth filter of 3 reads, which...

Thank you very much for your response. My maps are still a bit messy. I used your pipeline to obtain the genotype likelihoods (GL) for Lep-MAP3 with Samtools: samtools mpileup -q 10 -Q10 -s $(cat sorted_bams)|java Pileup2Likelihoods [options] >post.txt Since I didn’t apply any of the usual filters I use for SNP calling, I think I need to add some filtering to improve my plots. I’m considering adding a read depth filter. Pileup2Likelihoods already has a minimum read depth filter of 3 reads, which...