User: miaowzai

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miaowzai130
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Posts by miaowzai

<prev • 38 results • page 1 of 4 • next >
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Comment: C: VCF file phasing by SHAPEIT
... I found the genetic map from 1KG Phase3 files under the IMPUTE2 ftp here: http://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3/ ...
written 6 weeks ago by miaowzai130
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Answer: A: BaseQRankSum and FS
... I haven't seen anyone using these two values for hard filtering. But BaseQRankSum is basically a z-score for base qualities of reference and alternative alleles. Having a BaseQRankSum close to 0 means the reference and alternative alleles have the same base qualities and having BaseQRankSum around 2 ...
written 6 months ago by miaowzai130
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Comment: C: ComBat correction with one batch containing only one sample - keep or remove?
... I use ComBat for batch effect removal, too. From my understanding, it removes the batch effect through adjusting the data mean and variance from different bathes. If one of your batches contains only one sample, there is no way that ComBat can remove the variance (since there is no variance), and it ...
written 6 months ago by miaowzai130
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Strange order of multi-allelic site in VCF file
... I have a VCF file and I found something strange at a multi-allelic site. The first few columns are: chr12 106633569 rs3088113 C T,G The QUAL is high and VQSR says PASS for this site. For the individual genotypes, there are (GT:AD:DP:GQ:PL): 0/1:34,1,36:71:99:957,1047,1737,0,687,586 ...
vcf written 6 months ago by miaowzai130
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Answer: A: Error while downloading data from database[EGA]
... I have been having this problem for a long time and now it is solved by using their python3 client. Try it here: https://ega-archive.org/download/downloader-quickguide-v3#downloadClient I am not entirely sure why the same downloading works with the pythong3 client but not with the other methods tho ...
written 8 months ago by miaowzai130
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Comment: C: relationship between DP and variant call quality
... finswimmer, thank you so much for the elaborate explanation. It really helps! I think I understood my plot corretly and I was having problem expressing what I thought in English. Yes, I have a lot of samples with no variant at these positions. My samples are divided as cases and controls, and most ...
written 10 months ago by miaowzai130
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Comment: C: Error while downloading data from database[EGA]
... I am having the exact same problem so I still haven't finished downloading the files. A few weeks ago, I had been contacting with the EGA staff for at least 20 emails and they were saying that they had a server issue. Need some solutions too! ...
written 10 months ago by miaowzai130
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Comment: C: relationship between DP and variant call quality
... Hi, I made these two graphs using a few variants (5 to 6) within one gene called UBB (I also checked a few other genes). There is no 1/1 genotypes of these variants. The distributions are from these few variants in many samples (~1000 samples, all are EUR). ...
written 10 months ago by miaowzai130
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Comment: C: relationship between DP and variant call quality
... OK. I will ask about it. Thank you so much! ...
written 10 months ago by miaowzai130
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Comment: C: relationship between DP and variant call quality
... Thank you so much for the explanation Kevin. I usually get VCF file from data provider so I haven't actually done variant calling myself. Many VCF files that I deal with have a lot of problems regarding variant quality and I do not always have access to the bam files. The only thing that I can do is ...
written 10 months ago by miaowzai130

Latest awards to miaowzai

Popular Question 4 weeks ago, created a question with more than 1,000 views. For what is 0 in the plink .bim file under allele1/2 column?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For what is 0 in the plink .bim file under allele1/2 column?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Popular Question 5 months ago, created a question with more than 1,000 views. For what is 0 in the plink .bim file under allele1/2 column?
Popular Question 5 months ago, created a question with more than 1,000 views. For how to find strand information for a list of SNPs?
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