Activity for Roy Francis
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Roy Francis posted a comment on a wiki page
Are the above instructions/dependencies/versions still valid for Dec 2018?
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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?
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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?
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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$fastOrderThread (Case Conflict).class Thx
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Hi, There are several conflicted copies of java class files in the bin directory. This probably doesn't affect the functioning of the program. But just so you know. Error (prastas-XPS13-9333's conflicted copy 2017-08-14).class LMPlot (prastas-XPS13-9333's conflicted copy 2017-08-14).class OrderFinder$fastOrderThread (Case Conflict).class Thx
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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
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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...
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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...
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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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