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Minos test data

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martinghunt edited this page Aug 9, 2022 · 1 revision

If you want to test your minos installation, it has built-in test data. This page describes how to get the data and then run the "adjudicate" task, and run the joint genotyping pipeline.

The idea is that the commands below should run without errors and make the output files. Any errors indicate a problem with the minos installation. Each command should only take a few seconds to run.

Get the data

Run this to get make a new directory called test, containing a toy data set:

minos get_test_data test

Change to the test directory:

cd test

Test the adjudicate task

The reference FASTA is in the file ref.fa. We have two VCF files called in.1.vcf and in.2.vcf.

Sample 1 has two FASTQ files (ie paired Illumina). Run the single sample "adjudicate" task on sample1:

minos adjudicate \
  --reads sample1.reads_1.fastq.gz \
  --reads sample1.reads_2.fastq.gz \
  OUT.sample1 ref.fa in.1.vcf in.2.vcf

That made a new directory called OUT.sample1. The adjudicated call set is in OUT.sample1/final.vcf. The VCF records should look like this:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Files/sample1.bam
ref	200	.	A	C	.	PASS	.	GT:DP:ALLELE_DP:FRS:COV_TOTAL:COV:GT_CONF:GT_CONF_PERCENTILE	1/1:26:0,26:1.0:26:0,26:196.11:46.74
ref	400	.	G	A	.	PASS	.	GT:DP:ALLELE_DP:FRS:COV_TOTAL:COV:GT_CONF:GT_CONF_PERCENTILE	1/1:28:0,28:1.0:28:0,28:208.48:57.79
ref	600	.	T	C	.	PASS	.	GT:DP:ALLELE_DP:FRS:COV_TOTAL:COV:GT_CONF:GT_CONF_PERCENTILE	0/0:27:27,0:1.0:27:27,0:202.31:52.22

The output VCF files for the remaining commands are similar - the contents don't really matter. The important thing is that the commands run without errors.

Sample 2 has just one FASTQ file. Run the single sample "adjudicate" task on sample2:

minos adjudicate \
  --reads sample2.reads.fastq.gz \
  OUT.sample2 ref.fa in.1.vcf in.2.vcf

That made a new directory called OUT.sample2. The adjudicated call set is in OUT.sample2/final.vcf.

Test the joint genotyping pipeline

This assumes that you have nextflow and ivcmerge installed, in addition to minos itself. You will need the two nextflow files from the minos repository, called nextflow/regenotype.config and nextflow/regenotype.nf.

Run the nextflow pipeline using the data in the file manifest.tsv, replacing /path/to/minos/nextflow/ with the correct path to your nextflow files:

nextflow run \
  -c /path/to/minos/nextflow/regenotype.config \
  -profile tiny \
  /path/to/minos/nextflow/regenotype.nf \
  --ref_fasta ref.fa \
  --manifest manifest.tsv \
  --outdir OUT.joint_geno

This makes a new directory called OUT.joint_geno. The final VCF file with calls from the two input samples is called OUT.joint_geno/merged.vcf.

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