User: miaowzai

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miaowzai100
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Posts by miaowzai

<prev • 37 results • page 1 of 4 • next >
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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 19 days ago by miaowzai100
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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 27 days ago by miaowzai100
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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 27 days ago by miaowzai100
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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 12 weeks ago by miaowzai100
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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 4 months ago by miaowzai100
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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 4 months ago by miaowzai100
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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 4 months ago by miaowzai100
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Comment: C: relationship between DP and variant call quality
... OK. I will ask about it. Thank you so much! ...
written 4 months ago by miaowzai100
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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 4 months ago by miaowzai100
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Comment: C: relationship between DP and variant call quality
... Thanks for the reply! I understand this is not strictly true. But according to the DP distributions in my data, those 0/0 calls with low DP seem to be false negative calls to me, i.e. some of them may be actually 0/1 but they are called 0/0 since there is no ALT reads aligned due to low coverage. In ...
written 4 months ago by miaowzai100

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Supporter 4 months ago, voted at least 25 times.

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