User: miaowzai

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miaowzai70
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Posts by miaowzai

<prev • 34 results • page 1 of 4 • next >
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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 14 days ago by miaowzai70
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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 8 weeks ago by miaowzai70
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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 8 weeks ago by miaowzai70
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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 8 weeks ago by miaowzai70
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Comment: C: relationship between DP and variant call quality
... OK. I will ask about it. Thank you so much! ...
written 8 weeks ago by miaowzai70
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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 8 weeks ago by miaowzai70
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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 8 weeks ago by miaowzai70
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Comment: C: relationship between DP and variant call quality
... Thank you! I have read this post. According to Kevin's idea, it's safe to use a low DP cutoff (e.g. 10 or 18 for 0/1 and 1/1) to get accurate calls. But for 0/0, we may need higher values. I was wondering how can I decide which value to use... Actually, when I thought about this again, it doens't m ...
written 8 weeks ago by miaowzai70
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relationship between DP and variant call quality
... I am doing fitering (quality control) of a VCF file from exome sequencing. I already filtered by the VQSR threshold and kept only PASS loci. When I was trying to decide the cutoff of "DP" to use, I encounter this strange case: In a few variants in one gene, I observe very different distributions o ...
read depth variant quality coverage dp written 8 weeks ago by miaowzai70 • updated 8 weeks ago by finswimmer5.5k
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Comment: C: differences in covered regions in exome and whole genome sequencing
... I only kept around 900 EUR individuals from my exome data and only the ~500 EUR from the 1000genomes data. One possible reason that I can think of is that my data has more people than 1000genomes, so maybe some variants are discovered even by exome sequencing but not covered in 1000genomes data. But ...
written 9 weeks ago by miaowzai70

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