User: mostafarafiepour
mostafarafiepour • 60
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Posts by mostafarafiepour
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... Hi all dear,
I have downloaded a database that is related to SNP-chip data. This database contains three files:
![enter image description here][1]
So, i want to Calculate heterozygosity for each SNPs. I use plink --make-bed --file Colli_buffalo_diversity --freqx --out Coli_freqx script to calcul ...
written 3 months ago by
mostafarafiepour • 60
0
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Comment:
C: Create a 3-D PCA
... Many thanks dear cpad0112 for your good advice. ...
written 3 months ago by
mostafarafiepour • 60
4
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... Hi all dear,
I have a PCA output:
Pop PC1 PC2 PC3 Population
EAZ01 0.0394502269547468 0.0483472562251034 -0.0803608526481478 EAZ
EAZ02 0.0504868156065647 0.0580742278257349 -0.107896355901351 EAZ
EAZ03 0.03740738709061 ...
written 3 months ago by
mostafarafiepour • 60
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... Hi all dear,
I want to calculating heterozygosity for each SNPs. After studying the plink guide, I have calculated the heterozygosity using the following script.
plink --make-bed --file purebred411_qc --freqx --out freqx_411
And I got this output:
CHR SNP A1 A2 C(HOM A1) C(HET) ...
written 3 months ago by
mostafarafiepour • 60
• updated
3 months ago by
Kevin Blighe ♦ 41k
0
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433
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Comment:
C: Common SNPs among all populations
... This code works well but with a small change.
$ bcftools view -i 'GT[0-9]="alt" && GT[10-19]="alt" && GT[20-29]="alt" && GT[30-39]="alt" && GT[40-49]="alt"' Final.vcf|grep -v "^#"|wc -l ...
written 4 months ago by
mostafarafiepour • 60
0
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2
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433
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2
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Comment:
C: Common SNPs among all populations
... I installed the suggested version, but when I run the script, it does not give me the output. And it only displays the content of my VCF file in a graphical and fast way. My expectation is that when i run the script, i will give the number of common PSNs between 5 populations.
i code run:
bcft ...
written 4 months ago by
mostafarafiepour • 60
0
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2
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433
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Comment:
C: Common SNPs among all populations
... I use bcftools/1.3.1 version. I only have this version on the server. ...
written 4 months ago by
mostafarafiepour • 60
0
votes
2
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433
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2
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Comment:
C: Common SNPs among all populations
... I run your script, but I encountered this error.
[filter.c:1379 filters_init1] Error: the tag "INFO/GT[1" is not defined in the VCF header
this is header my vcf file:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT EAZ01 EAZ02 EAZ03 EAZ04 EAZ06 EAZ08 EA ...
written 4 months ago by
mostafarafiepour • 60
0
votes
2
answers
433
views
2
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Comment:
C: Common SNPs among all populations
... Many thanks for your reply,
I saw the page you shared. And the only thing I can find is the option --exclude-positions-overlap. Can you guide me more precisely? ...
written 4 months ago by
mostafarafiepour • 60
4
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433
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... Hi all Dear,
I have a VCF file that contains approximately 20 millions SNPs. And my VCF file has 5 populations (KHUZ, MAZ, WAZ, EAZ and GIL), each population has 10 samples. So, I want to know how many SNPs are common between the 5 populations?
Best Regard ...
written 4 months ago by
mostafarafiepour • 60
• updated
4 months ago by
zx8754 ♦ 7.1k
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