User: ShirleyDai

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ShirleyDai40
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3 years, 9 months ago
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Posts by ShirleyDai

<prev • 38 results • page 1 of 4 • next >
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Answer: A: Infinium Global Screening Array-Why there are few rsids/chromosome positons with
... I guess these loci are multi-alleles. You can check them in NCBI-SNP. ...
written 7 months ago by ShirleyDai40
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Comment: C: beta coefficient for METAL input
... Hello. If I use log(OR) as EFFECT, do I need to convert OR's standard error (SE) as well? ...
written 2.3 years ago by ShirleyDai40
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Answer: A: Plink: Quick Way To Combine Two Datasets Using Only Common Markers
... why not use plink --merge-mode 1, which would output Consensus calls. ...
written 2.4 years ago by ShirleyDai40
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Comment: A: imputation only choose one population as reference panel
... Hi Peter, Please check this website. https://mathgen.stats.ox.ac.uk/impute/using_multi_population_reference_panels.html I have also been confused about this for a long time. As I understand, before 1000Gp1v3, it is suggested to use "best match" population as reference. However, nowadays, for "moder ...
written 2.5 years ago by ShirleyDai40
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Answer: A: Metal - the commnad you issued could not be processed
... I guess you would like to run ./metal first. Then here's my script, and it worked. MARKER name ALLELE A1 A2 EFFECT beta_SNP_add STDERR sebeta_SNP_add PVAL p.val WEIGHTLABEL n FREQLABEL Freq1 MINMAXFREQ ON AVERAGEFREQ ON PROCESS file1.tx ...
written 2.6 years ago by ShirleyDai40
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Answer: A: Get Rs Number Based On Position (6 million SNPs)
... Hello, I just saw your output from METAL has the column "CHR" and "BP". Can you post you metal script as how to add these two variables to the result file. Because I have searched the whole website but cannot find a solution, so I came here to ask if you can help... Thanks Shirley ...
written 2.6 years ago by ShirleyDai40
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Comment: C: Any better ways to filter GATK Mutect2 output?
... Thanks. MAF filtering might be helpful. I'm calling somatic mutation from whole exome sequencing data of skin cancer. ...
written 2.8 years ago by ShirleyDai40
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Comment: C: Any better ways to filter GATK Mutect2 output?
... Mutect2 can be only used for somatic mutation calling, not germline. I have not try other tools yet. ...
written 2.8 years ago by ShirleyDai40
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Comment: C: Can I use exome sequencing data from cancer patient's blood to call germline var
... Then if I want to get all SNPs for whole genome, can I do imputation after genotype detection? ...
written 2.9 years ago by ShirleyDai40
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Comment: C: Can I use exome sequencing data from cancer patient's blood to call germline var
... Is there a way I can calculate normal purity from BAM files? ...
written 2.9 years ago by ShirleyDai40

Latest awards to ShirleyDai

Great Question 12 weeks ago, created a question with more than 5,000 views. For Any better ways to filter GATK Mutect2 output?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to run MutSigCV example correctly
Popular Question 6 months ago, created a question with more than 1,000 views. For How to run MutSigCV example correctly
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Popular Question 23 months ago, created a question with more than 1,000 views. For How to run MutSigCV example correctly
Popular Question 23 months ago, created a question with more than 1,000 views. For How to prepare WEGO input files
Popular Question 23 months ago, created a question with more than 1,000 views. For How to extract both start and end position in vcf files
Popular Question 23 months ago, created a question with more than 1,000 views. For errors in running smartpca
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Any better ways to filter GATK Mutect2 output?

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