User: waqasnayab

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waqasnayab180
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Pakistan
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7 months ago
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Posts by waqasnayab

<prev • 90 results • page 1 of 9 • next >
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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 7 months ago by waqasnayab180 • updated 7 months ago by genomax70k
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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 8 months ago by waqasnayab180 • updated 8 months ago by Pierre Lindenbaum121k
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Comment: C: Inversion validation / confirmation
... Thanks Kevin, I will try to share this information with my colleagues,!!!! ...
written 11 months ago by waqasnayab180
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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 11 months ago by waqasnayab180
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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 11 months ago by waqasnayab180 • updated 11 months ago by Kevin Blighe46k
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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 14 months ago by waqasnayab180
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VCFTOOLS --recode and --recode-INFO-all
... Hi, I am struggling with one the options of vcftools: I run the following command: vcftools --vcf ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf --keep eur_samples_ids.txt --recode --recode-INFO-all --out ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genot ...
gene vcf snp written 14 months ago by waqasnayab180 • updated 14 months ago by Kevin Blighe46k
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Comment: C: grep invert match - not working fine
... Yes, Pierre, there is A97, thats why, the desired record had been removed. I changed Kevin's command: awk '!index($3, $4) { print }' test.tsv | grep -v -f matches.list to: awk '!index($3, $4) { print }' test.tsv | grep -w -v -f matches.list and now the output has all the records that were remov ...
written 18 months ago by waqasnayab180
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Comment: C: grep invert match - not working fine
... I tried your command. Instead of getting colored T35, I got following line: chr15 41342365 rs7178634 A G NUSAP1 exonic NUSAP1 . nonsynonymous_SNV NUSAP1:NM_001243142:exon2:c.A97G:p.T35A,NUSAP1:NM_001243143:exon2:c.A97G:p.T35A,NUSAP1:NM_001301136:exon2:c.A97G:p.T35A,NUSAP1:NM_016359:exon2:c.A97G ...
written 18 months ago by waqasnayab180
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grep invert match - not working fine
... Hi, My this post is in continuation to my previous post: https://www.biostars.org/p/271265/ So, I am skipping some file introductory part. As Kevin replied with two commands. The second command: awk '!index($3, $4) { print }' test.tsv | grep -v -f matches.list here `grep -v` is supposed to d ...
software error genome snp written 18 months ago by waqasnayab180

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Popular Question 8 months ago, created a question with more than 1,000 views. For Downloading rice chloroplast genome
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