User: waqasnayab

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waqasnayab200
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Pakistan
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3 weeks ago
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Posts by waqasnayab

<prev • 94 results • page 1 of 10 • next >
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Batch rsIDS Allele Frequency Only Retrieval
... Hi, On > https://www.ncbi.nlm.nih.gov/books/NBK44444/#Search.how_do_i_get_snp_frequency_inform it is mentioned: > How do I get SNP frequency information using a batch query? Frequency > information is located in the genotype report. Please use the batch > query and select genotypeRe ...
next-gen snp sequencing written 7 weeks ago by waqasnayab200
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Comment: C: removing rows if X percentages of columns / fields are epmty
... This worked for me: awk '(NF==12){print}' all_sample_nomismatch.feature Now, I have all those columns (including columns 1 and 2 must, and then 3 to 22) where 3 to 22 fields are 50 percent filled. Hope I did correctly. Regards, Waqas. ...
written 11 weeks ago by waqasnayab200
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Answer: A: removing rows if X percentages of columns / fields are epmty
... Thanks Pierre, Yeah, I run the following command: awk '{W=0.0;for(i=3;i<=NF;i++) {if($i=="") W++;} if(W/(NF-3) <0.5) print; }' all_sample_nomismatch.feature and got this error: awk: cmd. line:1: (FILENAME=all_sample_nomismatch.feature FNR=1) fatal: division by zero attempted My i ...
written 11 weeks ago by waqasnayab200
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removing rows if X percentages of columns / fields are empty
... Hi, I have a tabular text file with 105078 rows and 22 columns I want to remove all those lines if 50 percent of columns (columns 3 - 22) has empty fields. I tried ISBLANK and IF function in excel, no luck. Could awk or sed help me? Regards, Waqas. Edited: tags and Spelling mistake ...
next-gen sed snp awk written 12 weeks ago by waqasnayab200 • updated 11 weeks ago by cpad011213k
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Haplotype frequency - High Regional HF
... Hi, I have a question of general type. What would be the reason if the occurrence of minor haplotype frequency (say 0.01) is higher in local/regional population (say 0.07)? selective breeding, linkage disequilibrium, etc., Thanks, Waqas. ...
allele frequency halpotype snp written 19 months ago by waqasnayab200 • updated 19 months ago by genomax87k
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Filtering of VCF, INFO DP or FORMAT DP
... Hi, I have a confusion regarding the filtering of VCF file. Consider the line below: chr1 14464 rs546169444 A T 112.33 . AC=1;AF=0.125;AN=8;BaseQRankSum=0.548;ClippingRankSum=0.000;DB;DP=123;ExcessHet=3.0103;FS=1.574;MLEAC=1;MLEAF=0.125;MQ=28.09;MQRankSum=0.745;QD=2.88;ReadPosRankSum=2.036;SOR ...
vcf next-gen dp snp sequencing written 20 months ago by waqasnayab200 • updated 20 months ago by Pierre Lindenbaum129k
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Comment: C: Inversion validation / confirmation
... Thanks Kevin, I will try to share this information with my colleagues,!!!! ...
written 23 months ago by waqasnayab200
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Comment: C: Inversion validation / confirmation
... By delly, as far as running delly on control samples is concerned, I have only subset of those bam files (means around my inversion region), and when I run delly, empty bcf file is generated. Might delly needs at least full chromosome...... Any thing which I can do? ...
written 24 months ago by waqasnayab200
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Inversion validation / confirmation
... Hi, I am wondering how to validate / confirm the existence of inversion region in other WGS samples? For example, in one of my patient's WGS sample, I identified an inversion. Now, I want to see whether this inversion exists in other WGS samples of healthy individuals or not (I have a control data ...
genome next-gen structural variant inversion written 24 months ago by waqasnayab200 • updated 24 months ago by Kevin Blighe63k
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Comment: C: VCFTOOLS --recode and --recode-INFO-all
... Hi Kevin, Nice to see your reply. It worked for me. I got updated `AC` and `AN` but not `AF`. As `AF` is dependent on `AC` and `AN`, `AF` should be changed in the output. Might be I am tooo stringent..,,!!!! or if there is a way to do that, Thanks, Waqas. ...
written 2.2 years ago by waqasnayab200

Latest awards to waqasnayab

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