Tag: Shapeit

Genetic footprints of assortative mating in the Japanese population

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

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Where To Get The Genetic Map For The Haplotype Reference Consortium to phase the data externally using SHAPEIT software with family information

Where To Get The Genetic Map For The Haplotype Reference Consortium to phase the data externally using SHAPEIT software with family information 0 The Sanger Imputation Service does not offer a pipeline that utilizes the family information during phasing. Therefore, our pipeline (previously) has been to previously use genetic maps…

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SHAPEIT phased haps file does not contain my SNPs of interest

SHAPEIT phased haps file does not contain my SNPs of interest 0 I produced a haps file using SHAPEIT, as below. However, when I query it to look for my 12 SNPs of interest, only 3 are in there. Does anyone know why? (PS they are not in the snp.strand.exclude…

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Convert SHAPEIT haps file to vcf

Convert SHAPEIT haps file to vcf 0 I’ve phased some sequencing using SHAPEIT, producing two files: 125QiPSC.haps 125QiPSC.log I would now like to subset the file for my SNPs of interest. To achieve this, I’m first attempting to convert it to a vcf. The SHAPEIT manual suggests this can be…

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SHAPEIT using VCF unphased genotype input

I can get SHAPEIT to work with the default Plink PED/MAP format input files, but not with a VCF as input. As an example, here I use the demo data that comes with SHAPEIT, which runs well. DEMO=/Users/michaelflower/bin/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64/example shapeit -B $DEMO/gwas.bed $DEMO/gwas.bim $DEMO/gwas.fam -M $DEMO/genetic_map.txt -O “$DIR”/shapeit/gwas.phased However, when I…

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phasing VCF files with missing genotype

phasing VCF files with missing genotype 0 I want to phasing a VCF file with missing value(./.), the output I want get (a VCF also)is all the genotype are phased, but the ./. will not be imputed. I have tried shapeit and beagle, but both of them impute the missing…

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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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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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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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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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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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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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