User: miaowzai

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miaowzai230
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Posts by miaowzai

<prev • 40 results • page 2 of 4 • next >
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Comment: C: relationship between DP and variant call quality
... OK. I will ask about it. Thank you so much! ...
written 23 months ago by miaowzai230
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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 23 months ago by miaowzai230
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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 23 months ago by miaowzai230
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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 23 months ago by miaowzai230
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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 23 months ago by miaowzai230 • updated 23 months ago by finswimmer13k
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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 23 months ago by miaowzai230
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(Closed) differences in covered regions in exome and whole genome sequencing
... I have a VCF dataset from whole exome sequencing of a cohort of people. I was considering to take some people from 1000genomes data and add them to my data so that I have a bigger cohort. To make the data (variant loci) consistent, I subsetted the 1000genomes data by the variants positions from my ...
genome-sequencing wgs exome-sequencing wes written 23 months ago by miaowzai230 • updated 4 months ago by Biostar ♦♦ 20
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Answer: C: strand information for SNPs from VCF file (convert into IMPUTE format)
... I found a tool to do this: https://github.com/biocore-ntnu/snpflip ...
written 2.2 years ago by miaowzai230
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Comment: C: Illumina exome beadchip duplicated positions
... This makes a lot of sense! Thank you so much. ...
written 2.2 years ago by miaowzai230
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Illumina exome beadchip duplicated positions
... I have a plink format data (bim/bed/fam) from data provider. As far as I know, the sequencing was done by Illumina exome SNP beadchip. I didn't call the genotypes. There are some variant IDs startwith "exm". They do have rs numbers when I look'em up. What are these SNPs? Why use "exm"? Also, I fou ...
exome illumina snp beadchip written 2.2 years ago by miaowzai230

Latest awards to miaowzai

Scholar 7 months ago, created an answer that has been accepted. For C: strand information for SNPs from VCF file (convert into IMPUTE format)
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Appreciated 11 months ago, created a post with more than 5 votes. For A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Popular Question 11 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 13 months ago, created a question with more than 1,000 views. For subseting VCF by bcftools
Popular Question 14 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 14 months ago, created a question with more than 1,000 views. For what is 0 in the plink .bim file under allele1/2 column?
Teacher 14 months 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 19 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 19 months ago, created a question with more than 1,000 views. For how to find strand information for a list of SNPs?
Supporter 23 months ago, voted at least 25 times.

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