Are the above instructions/dependencies/versions still valid for Dec 2018?
I ran SeparateChromosomes2 on my dataset like so: java -cp ~/ngs/programs/lep-map3/bin/ SeparateChromosomes2 data="snp-2.txt" lodLimit=10 theta=0.03 numThreads=8 subsample=0.25 > "snp-3-ss.txt" With the subsample argument, my idea was to use 25% of the total number of SNPs. But my output file has the same number of lines are the original number of SNPs. The output is mostly zeros. Only 4% of the rows have an integer other than zero. 0 0 0 0 0 1513 0 0 0 ... What does this mean?
I have too many markers (2 million or so). I am considering evenly thinning down to 100,000 markers or so (1 snp every kb for example). Then create the linkage map with the reduced set. In the end, can I interpolate the rest of the markers for higher density?
Hi, There are a few conflicted copies of java class files in the bin directory. This probably doesn't affect the functioning of the program. But just so you know. Error (prastas-XPS13-9333's conflicted copy 2017-08-14).class LMPlot (prastas-XPS13-9333's conflicted copy 2017-08-14).class OrderFinder$fastOrderThread (Case Conflict).class Thx
Hi, There are several conflicted copies of java class files in the bin directory. This probably doesn't affect the functioning of the program. But just so you know. Error (prastas-XPS13-9333's conflicted copy 2017-08-14).class LMPlot (prastas-XPS13-9333's conflicted copy 2017-08-14).class OrderFinder$fastOrderThread (Case Conflict).class Thx
Hi, Could you please provide example run times for these tools? ParentCall2 Filtering2 SeparateChromosomes2 JoinSingles2All OrderMarkers2 Just a rough idea like is it 10 mins or 10 hours for x number of markers and y number of samples. Thanks
Ah finally! I got ParentCall2 to work. I've been on this for a week. I've seen this add "CHR and POS" to it. I didn't know it was just about LITERALLY adding those strings. I 've been trying to figure out how CHR (chr1, chr2, chr3 etc) and POS (112343 etc) could possibly be associated with a pedigree. This is such a simple step but so confusing. I think ParentCall2 should have an argument that takes a normal pedigree file. I call it 'normal' because it is used by GATK and PLINK and so many other...
Hi, I have VCF v4.2 coming from GATK variant calling pipeline. Below is an example showing the first 3 SNPs for 4 samples. ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> ##FILTER=<ID=LowQual,Description="Low quality"> ##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39912.34"> ##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth...
Hi, I have VCF v4.2 coming from GATK variant calling pipeline. Below is an example showing the first SNP for 4 samples. ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> ##FILTER=<ID=LowQual,Description="Low quality"> ##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39912.34"> ##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth...
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