User: yolek64754

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yolek6475430
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Posts by yolek64754

<prev • 7 results • page 1 of 1 • next >
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How to compute Pi using VCFtools
... Hi there, I have been trying to compute "Pi" on my Ch22 using VCFtools; this is the pipeline I am using: Data=$1 bcftools mpileup --ignore-RG -f /ref/human_g1k_v37.fa.gz $Data | bcftools call -m -Oz -f GQ -o $Data"_ND.vcf.gz" zcat $Data"_ND.vcf.gz" | vcftools --vcf - --site ...
pi vcftools statistics written 15 days ago by yolek6475430
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Comment: C: Interpreting theta value
... I think in this way they use the prior knowing the reference true site ? I have no clear idea of it either but this is how I understand it. This is how the value fluctuates, doesn't really make sense to me either: -7.634670 -7.634670 -7.634670 -7.634670 -7.634670 -7.634670 -7.634670 -7.634670 -7.63 ...
written 19 days ago by yolek6475430
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Interpreting theta value
... Hi everyone, I have been computing Watterson theta for the first time and I am using [ANGSD][1] . For my understanding this value can be from 0 to 1. However on ANGSD use likelihood to run it and this is the results I have when I compute theta on Chr22 on one bamfile: (indexStart,indexStop)(fi ...
bioinformatics popgen statistics theta angsd written 19 days ago by yolek6475430
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Comment: C: BWA mem minimum read length
... Hi, I didn't mentioned it but the reads I am mapping are simulations and hence are not Ns. Thanks a lot, that could be an explanation for empirical data. ...
written 19 days ago by yolek6475430
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Watterson Theta with ANGSD [Segmentation Error]
... Hi everyone, I am trying to calculate Theta for the first time using ANGSD and this [tutorial][1] . I installed it using Conda (as I am running it on a cluster and don't want bother loading C packages to make and all). The first command `angsd -i MYsorted.bam -doSaf 1 -anc ref/human_g1k_v37.fa.g ...
theta watterson stats conda angsd written 20 days ago by yolek6475430 • updated 1 hour ago by Biostar ♦♦ 20
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Comment: C: BWA mem minimum read length
... Thanks for the quick answer. Yeah I don't use them in my analysis, I was just curious of why some reads of 36-38 bp mapped where none of 35 and below does. I was looking at the code and couldn't find any strict cutoff value so I was kinda lost but yeah I think it is probably some quality score becom ...
written 4 weeks ago by yolek6475430
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BWA mem minimum read length
... Hi everyone, I am currently mapping read from different read length (from 30 to 100) and I have been using BWA-mem and BWA-aln. I know that BWA-aln works better for those read's length but while I was analysing my bam files I realised that every reads < 35bp are set as "unmapped" by BWA-mem. So ...
short dna alignment bwa mem written 4 weeks ago by yolek6475430

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