how to get a summary of genotype file without using the GUI, only command lines ?

[Elise Albert]

Hello,

I am using Tassel 5 on a hpcc. I am allowed to submit jobs to the queue but not to run the GUI (or for a really short time with low memory allocation).

I sucessfully ran both step of the FILLIN procedure in order to impute my missing values in a matrix of 820 genotypes x 3 million SNPs.

# step 1

run_pipeline.pl -Xmx80g -FILLINFindHaplotypesPlugin -hmp snp_matrix.vcf -o snp_matrix_haplotypes

# step 2

run_pipeline.pl -Xmx80g -FILLINImputationPlugin -hmp snp_matrix.vcf  -d snp_matrix_haplotypes -o snp_matrix_imputed.hmp.txt.gz

1/ I got many outputs from these both steps. I do not really understand them.

Where can I find a description of the outputs given by FILLIN step 1 and 2 and their  meaning ? In particular the file which look like a map ? What is the meaning of the different columns ?

Besides, I am missing information about how was sucessfull this procedure ? How many data are still missing ? What is the new maf after imputation across my SNPs matrix ? What is the way to get these informations, without running the GUI ?

I tried as follow :

run_pipeline.pl -Xmx80g -importGuess snp_matrix_imputed.hmp.txt.gz -genotypeSummary overall,site 

with snp_matrix_imputed.hmp.txt.gz being the file I got after FILLIN step1 and 2

I got the result below concerning number of SNPs per chromsome. But nothing about maf, rate of remaining missing data etc...

#Genotype Table Name: snp_matrix

#Number of Taxa: 814

#Number of Sites: 3147262

#Sites x Taxa: 2561871268

#Chromosomes...

#1: start site: 0 (123) last site: 781595 (30427176) total: 781596

#2: start site: 781596 (30566) last site: 1312598 (19697549) total: 531003

#3: start site: 1312599 (192) last site: 1924382 (23459627) total: 611784

#4: start site: 1924383 (1016) last site: 2437538 (18584896) total: 513156

#5: start site: 2437539 (53) last site: 3147261 (26975377) total: 709723

What is the appropriate command line to get something equivalent to the "geno summary" in the GUI as shown here https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/GenoSummary/GenoSummary, BUT using only command line interface ?

I hope you could help me with that.

Thank.

Best regards. 

Elise

[Terry Casstevens]

run_pipeline.pl -Xmx80g -importGuess snp_matrix_imputed.hmp.txt.gz
-genotypeSummary overall,site -export genotypeSummary

It will produce multiple files

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