Category: Shapeit

Removing indels +/- a buffer area? How? : bioinformatics

Hey everyone. Hopefully an easy question but my Googling and looking for papers hasn’t really come up with much. I am using a software (IBDMix) to analyze some Neanderthal DNA vs. Modern humans using the new HG38 1000 Genomes data from earlier this year. The method in the IBDMix paper…

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Phasing using SHAPEIT

Hello, I need to use SHAPEIT for phasing only since I will conduct CH (compound heterozygous) analysis for recessive rare variant.. I will not perform imputation.  I am running SHAPEIT, and I see in the log file it says: Parameters :  * Seed : 1442251531  * Parallelisation: 12 threads  *…

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How long does it take to carry out the GWAS workflow?

How long does it take to carry out the GWAS workflow? 0 Including these steps: 1) raw data format transformation for five companies 2) update positions for all SNPs to hg37 version 3) Quality control within companies 4) Pre-phasing (SHAPEIT2) and imputation (IMPUTE2) for all SNPs of each company 5)…

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command not found, in IMPUTE2

Edit June 7, 2020: The code below is for phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs. For the initial pre-phasing process with SHAPEIT2, see my answer here: Phasing with SHAPEIT So, the steps are usually: pre-phasing into pre-existing haplotypes available from HERE ( Phasing…

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very high Ne close to present

MSMC: very high Ne close to present 1 Hello, I have a weird problem with MSMC2. I use it to study demography of a non-model species, with populations diverged over the last 100,000-1M years (the times are deeper than for the usual human work). In almost all cases, MSMC based…

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Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)

NB – Update July 29, 2020 – this thread will no longer be watched and, for all intents and purposes, will now be archived NB – Version 2 of tutorial can be found here and should be used going forward –> Produce PCA bi-plot for 1000 Genomes Phase III –…

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Where to find 1000 Genome phase 3 whole genome data and select only European population

Where to find 1000 Genome phase 3 whole genome data and select only European population 2 Hello: I was trying to download whole genome data from 1000Genome phase 3 data and extract only the EUR population (GBR, TSI, FIN, IBS, CEU). I used the ftp site: ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz, but apparently it…

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Losing ~60% of variants from sequence data after phasing with SHAPEIT

Losing ~60% of variants from sequence data after phasing with SHAPEIT 0 I have a sequenced locus on chromosome 9 that I am attempting to phase with SHAPEIT. My original vcf file has1617 variants. After phasing with SHAPEIT I am left with only 513 variants. I made sure to check…

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IMPUTE2 -merge_ref_panels

IMPUTE2 -merge_ref_panels 0 Hi all, i am trying to use IMPUTE2 with 2 reference panels to be merged. i am applying the code as per the example provided on IMPUTE2 page. but somehow the merged reference panel doesnt get produced (the REF file as per the example). any ideas? for…

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selscan not outputting ihs

selscan not outputting ihs 2 Hi all, I’m trying to calculate iHS with selscan: the program seems to apparently run normal, but my output file is empty. I’ve phased my data with SHAPEIT and tried the following commands: selscan –ihs –vcf input.phased.vcf –map input.phased.map –out output.phased selscan –ihs –hap input.phased.haps…

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Phasing with SHAPEIT

Edit June 7, 2020: The code below is for pre-phasing with SHAPEIT2. For phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs, see my answer here: A: ERROR: You must specify a valid interval for imputation using the -int argument, So, the steps are usually: pre-phasing…

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Produce PCA bi-plot for 1000 Genomes Phase III

Note1 – Previous version: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old) Note2 – this data is for hg19 / GRCh37 Note3 – GRCh38 data is available HERE The tutorial has been updated based on the 1000 Genomes Phase III imputed genotypes. The original tutorial was…

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Phasing and imputation with Shapeit

Phasing and imputation with Shapeit 0 Hi, I wish to do some imputation and phasing analysis using Shapeit. This is my first time. I have bovine data (1 – 29 chromosomes) in VCF format. I have reference population with 4k animals and 10k animals to be imputed for about 23k…

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Output per variant and per sample heterozygosity fraction from VCF.

Output per variant and per sample heterozygosity fraction from VCF. 2 As a QC measure I would like to know the per variant and per sample heterozygosity fraction. I already used vcftools to output the missingness per variant and sample. vcftools.github.io/man_latest.html Is there any tool that can do the same…

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What is the best software for “phasing” in human population genomics with trio family pedigree?

What is the best software for “phasing” in human population genomics with trio family pedigree? 0 Hi, I am new to bioinformatics. Currently I have the a list of identified SNPs from trio human population. I am planning to do phasing to figure out the proportion of the SNPs coming…

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VCF file phasing by SHAPEIT

Hi everybody, I would like to phase (just phasing, not imputation) vcf file containing about 1100 individuals (a given human population) derived from whole genome sequencing, the vcf file obtained by GATK. As I searched, SHAPEIT was mostly used; based on its manual, it requires genetic map for phasing, however,…

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phasing with shapeit for non human spicies

phasing with shapeit for non human spicies 0 I am trying to phase genotyping data in non-human organism. I have a reference for my plant species only in fasta format, but required input for shapeit are phased.gz legend.gz and .sample how can I do phasing with my reference panel? Any…

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