User: ShirleyDai
ShirleyDai • 40
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Posts by ShirleyDai
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... I guess these loci are multi-alleles. You can check them in NCBI-SNP. ...
written 17 months ago by
ShirleyDai • 40
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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 3.2 years ago by
ShirleyDai • 40
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... why not use plink --merge-mode 1, which would output Consensus calls.
...
written 3.2 years ago by
ShirleyDai • 40
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... 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 3.4 years ago by
ShirleyDai • 40
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... 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 3.4 years ago by
ShirleyDai • 40
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... 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 3.4 years ago by
ShirleyDai • 40
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... Thanks. MAF filtering might be helpful.
I'm calling somatic mutation from whole exome sequencing data of skin cancer.
...
written 3.6 years ago by
ShirleyDai • 40
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... Mutect2 can be only used for somatic mutation calling, not germline.
I have not try other tools yet. ...
written 3.6 years ago by
ShirleyDai • 40
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... Then if I want to get all SNPs for whole genome, can I do imputation after genotype detection? ...
written 3.7 years ago by
ShirleyDai • 40
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... Is there a way I can calculate normal purity from BAM files? ...
written 3.7 years ago by
ShirleyDai • 40
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