You did run the shapeit program, but without any input options, it won't do anything. However, unlike most programs, it doesn't tell you this, or tell you what the options actually are, unless you ask it to.

If you run ./shapeit --help you will see all the options available for running this program.

Segmented HAPlotype Estimation & Imputation Tool

* Authors : Olivier Delaneau, Jared O'Connell, Jean-François Zagury, Jonathan Marchini

* Contact : send an email to the OXSTATGEN mail list https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=OXSTATGEN

* Webpage : https://mathgen.stats.ox.ac.uk/shapeit

* Version : v2.r904

Basic options:

-H [ --help ] Produce help message.

--licence Produce licence description.

--version Produce version number.

--source Produce source file version details.

--seed arg (=1560157373) Seed of the random number generator.

--aligned Ref allele is aligned on the reference

genome

-T [ --thread ] arg (=1) Number of thread used for phasing.

-L [ --output-log ] arg (=shapeit_date_time_UUID.log)

Log file containing a copy of the

screen output.

Subsetting options:

--exclude-snp arg List of positions to exclude in

input/output files.

--include-snp arg List of positions to include in

input/output files.

--exclude-ind arg List of samples to exclude in

input/output files.

--include-ind arg List of samples to include in

input/output files.

--exclude-grp arg List of populations to exclude in input

files. Works only on the reference

panel of haplotypes.

--include-grp arg List of populations to include in input

files. Works only on the reference

panel of haplotypes.

--input-from arg (=0) First physical position to consider in

input files.

--input-to arg (=1000000000) Last physical position to consider in

input file.

--output-from arg (=0) First physical position to output.

--output-to arg (=1000000000) Last physical position to output.

Input files options:

-P [ --input-ped ] arg Unphased genotypes in PED/MAP format.

--missing-code arg (=0) Missing data character in PED/MAP

format.

-B [ --input-bed ] arg Unphased genotypes in BED/BIM/FAM

format.

--noped No pedigree information taken into

account.

--duohmm Phase pedigrees using the duoHMM

algorithm.

-G [ --input-gen ] arg Unphased genotypes in GEN/SAMPLE

format.

--input-thr arg (=0.9) Probability threshold used to call

genotypes in GEN file.

-V [ --input-vcf ] arg Unphased genotypes in VCF format.

-M [ --input-map ] arg Genetic map in HapMap format.

-R [ --input-ref ] arg Reference set of haplotypes in

HAPS/SAMPLE format.

--input-init arg Phased haplotypes in HAPS/SAMPLE format

used for initialisation.

- [ --input-sex ] arg Sex of the samples.

--missing-maf MAF based initialisation of missing

genotypes prior to phasing

-X [ --chrX ] Unphased genotypes are from chromosome

X non autosomal region.

--force proceed with phasing regardless of QC

warnings.

MCMC options:

--burn arg (=7) Number of burn-in MCMC iterations.

--prune arg (=8) Number of pruning MCMC iterations.

--main arg (=20) Number of main MCMC iterations.

--run arg (=1) Number of pruning stages

--no-mcmc No MCMC iteration (just phase given the

reference panel haplotypes).

Model options:

-S [ --states ] arg (=100) Number of hidden states used for

phasing (selected using Hamming

distance minimisation).

--states-random arg (=0) Number of hidden states used for

phasing (selected at random).

--states-pmatch arg (=0) Number of hidden states used for

phasing (selected using perfect match

maximisation).

--states-cov arg (=0) Number of hidden states used for

phasing (selected using perfect match

that maximise coverage of the region).

-W [ --window ] arg (=2) Mean size of the windows in which

conditioning haplotypes are defined.

--model-version1 Use the graphical model to represent

the conditioning haplotypes (as in

SHAPEIT v1).

--effective-size arg (=15000) Effective size of the population.

--rho arg (=0.0004) Constant recombination rate.

--input-copy-states arg To specify who to copy from

Output file options:

-O [ --output-max ] arg Phased haplotypes in HAPS/SAMPLE format.

--output-graph arg Phased haplotype graphs in binary format (v2.2).

Its working now

Thank you ,dear Thomas Lopdell

dear Thomas Lopdell

I entered the command as you said, but the result was not exactly the same as your result.

the result of my running is the more summary than your running, the result of my running is as follows:

Segmented HAPlotype Estimation & Imputation Tool

* Authors : Olivier Delaneau, Jared O'Connell, Jean-François Zagury, Jonathan Marchini

* Contact : send an email to the OXSTATGEN mail list https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=OXSTATGEN

* Webpage : https://mathgen.stats.ox.ac.uk/shapeit

* Version : v2.r904

ERROR: You must specify at least one unphased input file with --input-bed, --input-ped, -- input-gen or -- input-vcf

Also, when I entered the example of instance on the University of Oxford website, the system did not do it and make some error.

What is the reason?

I also transferred the input files with specified format to the folder bin that SHAPEIT software was in it, but returned some error.

Best regards

Hi Farhad Alizadeh,

I think the reason is that you have an extra space in the option name: you wrote '-- help' rather than '--help'. In Linux commands, the option '--' often signifies that there are no more options following, so everything else will be treated as a file name.

Dear Thomas Lopdell

Its working now.

You've helped me a lot, Thank you .