svmu
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mahulchak
A program to call variants from genome alignment
I am running an analysis on two genomes - one with a pseudochromosome level assembly, the other with a scaffold level assembly. Using the provided command for lastz took several...
HI! SVMU is a very good tools to detect SVs comparing others. My code is "svmu ref_qry.filted.delta ref.fa qry.fa l null ref_qry" , but some “sv.prefix.txt” is empty with [0.4-alpha](https://github.com/mahulchak/svmu/tree/0.4-alpha)...
Hello, I used SVMU for SV detection based on mummer result and found that in the sv.prefix.txt file, the length of CNV in both reference and query genomes were the...
I got en error ruining your svmu: ``` svmu sam2ref.mr.delta ref.fa query.fa 100 h > sample.small.txt ``` Error： ``` terminate called after throwing an instance of 'std::invalid_argument' what(): stoi Aborted...
Hi! SVMU is a pretty good tools to detect SVs. But I am be confused about the result files, the sv.xxx.txt and cnv.xxx.txt. In my understanding, CNVs are some types...
Hi, I would like to ask you about two small problems encountered when running svmu. Here's the script I used: **nucmer --mum -p out msu.Chr6.fa r498.Chr6.fa delta-filter -i 80 -1...
When I run step "make", I get error like this ![Uploading error.png…]() g++ -g -Wall -std=c++0x -c svlib.cpp svlib.cpp:4: error: expected nested-name-specifier before ‘chroms’ svlib.cpp:4: error: ‘chroms’ has not been...
Hello, I'm encountering an issue that several people have raised here but I can't find how they fixed it I am not able to run lastZ because the genomes are...
Hello professor: When I use the lastz to get *_lastz.txt file using `lastz *.genomic.fa[multiple] *.genomic.fa[multiple] --chain --format=general:name1,strand1,start1,end1,name2,strand2,start2,end2 > *_lastz.txt` some problem like below happen: "FAILURE: in add_segment() table size (4,869,542,152...
