User: wanabi

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wanabi60
Reputation:
60
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New User
Location:
Germany
Last seen:
1 year, 9 months ago
Joined:
4 years, 1 month ago
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s************@gmail.com

Posts by wanabi

<prev • 12 results • page 1 of 2 • next >
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Calculate ROH in whole-genome sequencing data with plink1.9
... Hello, Which parameters do you recommend to call ROH in WGS data with plink? Thanks a lot. ...
wgs plink2 roh plink1.9 written 3.7 years ago by wanabi60
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SwiftLink .dat format
... Hello, I am planning to do linkage analysis on WES data using SwiftLink(https://github.com/ajm/swiftlink). For this I need three input files: pedigree file, map file and locus data file. Can someone explain me what the format of the later (data file) should be? In the website there is an example fi ...
swiflink .dat format linkage analysis written 3.7 years ago by wanabi60 • updated 3.2 years ago by amedlar0
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XHMM on whole genome sequencing data
... Hello, Has anyone used XHMM for CNV detection in whole-genome sequencing data? I am planning to do this using a dummy capture kit containing all human exons. Is this reasonable? Thans ...
wgs whole-genome sequencing xhmm cnv written 3.7 years ago by wanabi60
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Comment: C: Linkage analysis with whole -exome sequencing data
... Thanks for your reply. However, I dont think you can do classical two-point or multi-point linkage analysis with PLINK or PLINK1.9 Thanks ...
written 3.7 years ago by wanabi60 • updated 14 months ago by RamRS24k
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Linkage analysis with whole -exome sequencing data
... Which software do you recommend to perform classic linkage on whole exome sequencing data?   Thanks ...
linkage whole exome sequencing written 3.7 years ago by wanabi60 • updated 14 months ago by nudrylab0
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Differences between SKAT.SSD.Al and SKATBinary.SSD.All
... Hello, there are two ways to perform a SKAT-O test with SKAT R package. Does anyone now the differences between the two options below?  1. SKAT.SSD.All(SSD.INFO,obj1,method="optimal.adj",obj.SNPWeight=Read_SNP_WeightFile(WEIGHTS)) 2. SKATBinary.SSD.All(SSD.INFO,obj2,method="SKATO",obj.SNPWeight=Re ...
skat skat-o skat test skat-o test written 3.8 years ago by wanabi60
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SKAT-O for recessive variants only
... Hello, I want to see if some genes of interest have an increased burden of alternative homozygous variants in cases versus controls. Is there an easy way to implement this in SKAT? Something I am considering doing is creating a dummy VCF file in which reference homozygous and heterozygous variants ...
skat skat-o written 3.8 years ago by wanabi60
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Regions of extreme GC content
... Hello for CNV analysis QC, I am looking for a reliable bed file of regions with extreme (>90%, <10%) GC content. Any idea were I can find such file? I tried UCSC but it gives it in bins of 5bp, which is not very convenient.   Thanks ...
gc content written 4.1 years ago by wanabi60 • updated 4.1 years ago by Devon Ryan92k
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Answer: A: Regions to exclude in CNV analysis
... Thanks a lot for the info. Do you know where I can get a similar file for extreme (>90, <10 GC content). Ucsc just provides 5bp tracks which are not very useful to filter out CNV data.   Thanks! ...
written 4.1 years ago by wanabi60
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Answer: A: Regions to exclude in CNV analysis
... Thanks for the info.   Yes, I am planning to exclude those regions either with plink or bedtools. My question is more about the lists of regions to exclude, and specially, about the threshold people use for regions with low mappability.   Thanks ...
written 4.1 years ago by wanabi60

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