How to calculate expected Heterozygosity of Haploid organism?

Hi all

Seeking alternative tools and information similar to Structure Harvester for population genetics analysis, as the tool's website is currently unavailable.

Any suggestions?

How can I construct a phylogenetic tree based on the SNP's shared between strains? I have whole genome SNP calls different strains in a multi-sample vcf. (raw fastq also)

Are there any tools that can take the vcf as an input for creating phylogenetic trees? Or do I need to convert the multi-sample vcf to another matrix? Which kind of matrix would that be how can I create it from the vcf?

Is there a list somewhere of popular packages that kan be used for creating phylogenetic trees? Or guides on how to go from a multi-sample vcf to a plylogenetic tree.

How to calculate heterozygosity ?

Hello. Everyone.

I have been calculating Fst of my sequencing result obtained from RADseq.

I've done variant calling using GATK and finished filtering step of some procedures with vcftools.

Anyhow, I made final vcf file having 138 variants.

I just wanted to know Fst between two different populations in that vcf file, and tried to gain the value using vcftools.

I ran the following command;

vcftools --gzvcf $in/FIN.vcf.gz --weir-fst-pop $pop/A.txt --weir-fst-pop $pop/B.txt --fst-window-size 10000 --out $pop/A-B

After that, I saw a results of something weird.

Using zlib version: 1.2.11

Warning: Expected at least 2 parts in FORMAT entry: ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

Keeping individuals in 'keep' list

After filtering, kept 20 out of 182 Individuals

Outputting Windowed Weir and Cockerham Fst estimates.

Weir and Cockerham mean Fst estimate: -nan

Weir and Cockerham weighted Fst estimate: -nan

After filtering, kept 168 out of a possible 168 Sites

Run Time = 0.00 seconds

Mean Fst and weighted Fst were all 'NaN'.

Have you ever seen this problem?

Although I have been searching to solve this problem and trying to modify based on the vcftools manual, I am still in fog.

If you guys know the way to breakthrough this problem, please be my light.

Thank you!

Hello all,

I have a file in STRUCTURE format (recode.strct_in) made with PLINK to filter by linkage disequilibrium to use in STRUCTURE software. Now I want to use this same matrix (in STRUCTURE format) as an input to PLINK in order to generate a .raw file. I have already tried with PGDSPIDER, but it only gives the .ped file but not the .map file, and both are necessary as an input to PLINK. Any suggestion on how can I solve this?

Thanks,

Ignacio

I have an RNA seq dataset. My samples are in columns (n=48) and my gene IDs are in rows (n=62976). Since my variable name are the RNAs, they should be as columns. Unfortunately, Excel does not support this size. I used t() function in R, but I don't know how I can introduce the previous first column (the new first row) as the vector name.

How to convert a VCF file into a FASTA file given a reference sequence using the abundant variants with Python?

Greetings!

I am dealing with NGS data. I have a vcf file of the called SNPs. I want to do population diversity and differentiation analysis with it but unfortunately, I unable to do so though I have tried using different software too. Can anyone help me in suggesting ways to do analysis using the vcf file?

I converted my genepop file into BAPS file using CREATE. I have read the manual yet unable to understand how to proceed further. Any recommendations would be helpful.