User: azmanr

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azmanr0
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Posts by azmanr

<prev • 5 results • page 1 of 1 • next >
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Comment: A: ENSEMBL VEP Inconsistent Results
... Hi Emily, Thanks for your response. My apologies I made that mistake previously and may have posted the wrong file. That being said, the incorrect file and the correct file are similar containing splice donor variants. Even with the incorrect file, I was using the same file for all my previous jobs ...
written 18 months ago by azmanr0
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ENSEMBL VEP Inconsistent Results
... For my chromosome 12 vcf zebrafish file I ran the online VEP tool last Friday and got some splice donor variants. I generated sequence around those mutations and ran BLAT to confirm their location as I was not getting location for most of my variants on the online list. When I downloaded the vcf fil ...
ensembl vep written 18 months ago by azmanr0
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Comment: C: Haplotype frequencies from 1000 genomes
... Okay, so when I use samtools phase to get two consensus sequences for each phase, does phase 0 correspond to the reference sequence while phase 1 is the alternate consensus sequence? It is my understanding that if I have a phased bam file I can get genotypes specific to a haplotype and can use samto ...
written 20 months ago by azmanr0
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Comment: A: Haplotype frequencies from 1000 genomes
... I used samtools phase to divide 1000 genomes bam files into phase 0 and 1. For one snp genotyped as GC, does phase 0 correspond to G and phase 1 correspond to C? ...
written 20 months ago by azmanr0
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Answer: A: Allele frequency of a gene from a .bam file.
... Hi, For one chromosome, I ran the command: samtools mpileup -ugf GRCz10.fasta mutant_chr12.bam | bcftools call -vm -o chr12.mut.raw.vcf I seem to have used the same options for mpileup and bcftools call, but I do not seem to get the AF field in my output vcf files. I do get the DP4 field nested i ...
written 21 months ago by azmanr0

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