How to run bcftools roh with multiple samples vcf

Question

[BAGeno]

Hi,

I am trying to run bcftools roh. I searched through this link and found it only mentioned about processing of 1000 genomes files. Bcftools roh calling

My problem is this I did not know how to use this command for my file. I tried to run this command with my file it gave me this error

bcftools roh --AF-file AF.txt -M 100 Input.vcf.gz > roh.txt

It gave me this error.

Missing the option -s, --sample

Can any please tell me how should I run command on multi-sample file?

Answer 1

[BioinfGuru]

The process of problem solving a command begins (and usually ends) with 2 steps: 1) View the help file 2) View the online docs

Start with the help function to see the usage and options for roh (works for most programmes) to give you a clue of what to do

bcftools roh --help

Notice the "usage" (how to use the funciton) + list of options:

Usage:   bcftools roh [options] <in.vcf.gz>

# some selected options
--AF-file <file>                   read allele frequencies from file (CHR\tPOS\tREF\tALT\tAF)
-M, --rec-rate <float>             constant recombination rate per bp
-s, --samples <list>               list of samples to analyze [all samples]
-S, --samples-file <file>          file of samples to analyze [all samples]
-o, --output <file>                write output to a file [standard output]

Learn how to understand the individual parts of your command by comparing it to the "Usage" and the other options in the --help output

bcftools roh --AF-file AF.txt -M 100 Input.vcf.gz > roh.txt # Your command
bcftools roh [options] <in.vcf.gz> # usage

Breakdown:

bcftools roh                       # tells the computer to run the roh function in the bcftools programme
--AF-file AF.txt                   # [option]: file containing read allele frequencies
-M 100                               # [option]: constant recombination rate per bp
Input.vcf.gz                        # <in.vcf.gz>: your compressed input vcf file

Now you should be able to conclude what is missing:

Error: Missing the option -s, --sample # so from --help, you are not providing a list of samples

So the next question is: what is "a list of samples"? For that, go find the online docs (just google "bcftools roh docs"):

BCFtools Manual page

Now look through the document for the more comprehensive explanation of how to provide the correct input for -s or -S

So to recap: Use --help, then find the manual for more detail.

[finswimmer]

Again I was to slow ;)

fin swimmer

[BAGeno]

@YaGalbi I already searched through options of bcftools roh and read bcftools manual pages but I did not see any option in bcftools roh manual in which we can specify many samples. Also I tried command with one sample name and it worked just fine. Here are the options when I tried bcftools roh help.

About:   HMM model for detecting runs of autozygosity.
Usage:   bcftools roh [options] <in.vcf.gz>

General Options:
        --AF-tag <TAG>                 use TAG for allele frequency
        --AF-file <file>               read allele frequencies from file (CHR\tPOS\tREF,ALT\tAF)
    -e, --estimate-AF <file>           calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>
    -G, --GTs-only <float>             use GTs, ignore PLs, use <float> for PL of unseen genotypes. Safe value to use is 30 to account for GT errors.
    -I, --skip-indels                  skip indels as their genotypes are enriched for errors
    -m, --genetic-map <file>           genetic map in IMPUTE2 format, single file or mask, where string "{CHROM}" is replaced with chromosome name
    -M, --rec-rate <float>             constant recombination rate per bp
    -r, --regions <region>             restrict to comma-separated list of regions
    -R, --regions-file <file>          restrict to regions listed in a file
    -s, --sample <sample>              sample to analyze
    -t, --targets <region>             similar to -r but streams rather than index-jumps
    -T, --targets-file <file>          similar to -R but streams rather than index-jumps

HMM Options:
    -a, --hw-to-az <float>             P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy-Weinberg) state [1e-8]
    -H, --az-to-hw <float>             P(HW|AZ) transition probability from HW to AZ state [1e-7]
    -V, --viterbi-training             perform Viterbi training to estimate transition probabilities

[finswimmer]

Hello,

check the version of your bcftools and update if necessary.

$ bcftools --version
bcftools 1.8
Using htslib 1.8
Copyright (C) 2016 Genome Research Ltd.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

fin swimmer

[BAGeno]

Thanks I checked and found I have bcftools 1.2

[finswimmer]

Then you have to update to at least 1.4. That's the first version where -S, --samples-file FILE appears in the manual.

Answer 2

[finswimmer]

Hello,

it seems that bcftools roh doesn't run automatically on all samples within the vcf. You have to specify the names of the samples either by using -s sample_name1,sample_name2 or -S list_with_sample_names.txt.

Have a look into the manual for further informations.

fin swimmer

[BAGeno]

I have tried already samples names with comma but it did not worked also I tried to run command with -S option it gave me error of roh: invalid option -- 'S'