User: mostafarafiepour

Reputation:
60
Status:
Trusted
Location:
Last seen:
4 days, 15 hours ago
Joined:
11 months, 2 weeks ago
Email:
m***************@yahoo.com

Posts by mostafarafiepour

<prev • 157 results • page 1 of 16 • next >
1
vote
0
answers
139
views
0
answers
Calculate heterozygosity for each SNPs in the bim file.
... 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 ...
snp-chip snp written 9 days ago by mostafarafiepour60
0
votes
1
answer
128
views
1
answers
Comment: C: Create a 3-D PCA
... Many thanks dear cpad0112 for your good advice. ...
written 11 days ago by mostafarafiepour60
4
votes
1
answer
128
views
1
answer
Create a 3-D PCA
... 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 ...
R written 11 days ago by mostafarafiepour60
1
vote
1
answer
180
views
1
answer
Calculating Heterozygosity for each SNPs.
... 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) ...
snp written 15 days ago by mostafarafiepour60 • updated 15 days ago by Kevin Blighe35k
0
votes
2
answers
278
views
2
answers
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 weeks ago by mostafarafiepour60
0
votes
2
answers
278
views
2
answers
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 weeks ago by mostafarafiepour60
0
votes
2
answers
278
views
2
answers
Comment: C: Common SNPs among all populations
... I use bcftools/1.3.1 version. I only have this version on the server. ...
written 4 weeks ago by mostafarafiepour60
0
votes
2
answers
278
views
2
answers
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 weeks ago by mostafarafiepour60
0
votes
2
answers
278
views
2
answers
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 5 weeks ago by mostafarafiepour60
4
votes
2
answers
278
views
2
answers
Common SNPs among all populations
... 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 ...
vcf snp written 5 weeks ago by mostafarafiepour60 • updated 4 weeks ago by zx87546.2k

Latest awards to mostafarafiepour

Centurion 12 weeks ago, created 100 posts.
Rising Star 8 months ago, created 50 posts within first three months of joining.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1100 users visited in the last hour