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getting_started.md

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Getting started with Tachyon

Table of contents

Workflow example: using the CLI

import: Importing VCF/BCF

Import a bcf file to yon with a block-size of -c number of variants and/or -C number of base-pairs. If both -c and -C are set then the block breaks whenever either condition is satisfied. Compression levels can be adjusted (-L) in the range 0 to 20 and corresponds to worse to better compression at a trade-off between compression time and file size. The decompression times virtually unaffected by the compression level chosen.

tachyon import -i examples/example_dataset.bcf -o example_dataset.yon -c 2000

Tachyon can protect your sensitive identifying information with high-grade encryption. By default, each data field is encrypted with a unique key in each block using AES-256. Simply pass the -e flag and the best practices will be used.

tachyon import -i examples/example_dataset.bcf -o example_dataset.yon -c 2000 -e

This will produce two output files:

  • example_dataset.yon
  • example_dataset.kyon

view: Viewing, converting, and slicing YON files

Printing a yon file as a bit-exact copy of the input VCF

tachyon view -i example_dataset.yon -H

Output

Contig110_arrow	672	.	A	T	525.07	basic_filtering	AC=10;AF=0.217;AN=46;BaseQRankSum=0.967;DP=72;ExcessHet=0.8113;FS=54.73;InbreedingCoeff=-0.0525;MLEAC=11;MLEAF=0.239;MQ=31.05;MQRankSum=1.38;QD=18.11;ReadPosRankSum=-0.431;SOR=5.889	GT:AD:DP:GQ:PL	0/0:1,0:1:3:0,3,38	1/1:0,2:.:6:76,6,0	./.:0,0:0:.:0,0,0	0/1:2,2:.:43:58,0,43	0/0:1,0:1:3:0,3,24	0/0:4,0:4:12:0,12,141	./.:0,0:0:.:0,0,0	0/0:1,0:1:3:0,3,29	0/1:1,4:.:19:147,0,19	0/1:3,2:.:49:71,0,49	0/0:5,0:5:0:0,0,81	./.:1,0:1:.:0,0,0	./.:0,0:0:.:0,0,0	0/0:6,0:6:18:0,18,192	1/1:0,2:.:6:58,6,0	0/0:1,0:1:3:0,3,11	./.:1,0:1:.:0,0,0	./.:0,0:0:.:0,0,0	0/1:3,2:.:58:58,0,63	./.:0,0:0:.:0,0,0	0/0:4,0:4:12:0,12,134	0/0:3,0:3:0:0,0,44	0/0:3,0:3:9:0,9,90	./.:0,0:0:.:0,0,0	./.:0,0:0:.:0,0,0	./.:0,0:0:.:0,0,0	0/0:2,0:2:6:0,6,53	0/1:1,2:.:19:62,0,19	0/0:3,0:3:9:0,9,84	0/0:2,0:2:6:0,6,49	0/1:1,2:.:19:74,0,19	0/0:1,0:1:3:0,3,38	./.:2,0:2:.:0,0,0	./.:0,0:0:.:0,0,0	0/0:2,0:2:6:0,6,65	./.:0,0:0:.:0,0,0

We can check for bit-exact output from tachyon by comparing the output of the cryptographic hash function SHA512 for bcftools. We drop the header -H as these two are different: both tools inject a timestamp and library versions each time a command is executed among other things.

tachyon view -i example_dataset.yon -H | openssl dgst -sha512
4c94ee35fa3509935e5ea63f6da9b39dc94b1073b551c7d4d56bca7666a6872ad629b6f91f43a8dc45b306c0b0bbb2f414fb811ed45c7e6434c3570b2e448c68

bcftools view example_dataset.bcf -H | openssl dgst -sha512
4c94ee35fa3509935e5ea63f6da9b39dc94b1073b551c7d4d56bca7666a6872ad629b6f91f43a8dc45b306c0b0bbb2f414fb811ed45c7e6434c3570b2e448c68

Listing only site-specific information and INFO fields:

tachyon view -i example_dataset.yon -GH

Output

Contig110_arrow	672	.	A	T	525.07	basic_filtering	AC=10;AF=0.217;AN=46;BaseQRankSum=0.967;DP=72;ExcessHet=0.8113;FS=54.73;InbreedingCoeff=-0.0525;MLEAC=11;MLEAF=0.239;MQ=31.05;MQRankSum=1.38;QD=18.11;ReadPosRankSum=-0.431;SOR=5.889

Field-slicing

Listing a specific INFO field with output data still adhering to the VCF specification:

tachyon view -i example_dataset.yon -GH -f "INFO=AC"

Output

Contig110_arrow	672	.	.	.	.	basic_filtering	AC=10

Add REF and ALT to the output

tachyon view -i example_dataset.yon -GH -f "INFO=AC;REF;ALT"

Output

Contig110_arrow	19575	.	A	C	.	basic_filtering	AC=2

Listing all available INFO fields and the FORMAT fields DP and PL in VCF

tachyon view -i example_dataset.yon -f "chrom;pos;ref;alt;info;format=dp,pl" -H -O vcf

Output

Contig110_arrow	672	.	A	T	.	basic_filtering	AC=10;AF=0.217;AN=46;BaseQRankSum=0.967;DP=72;ExcessHet=0.8113;FS=54.73;InbreedingCoeff=-0.0525;MLEAC=11;MLEAF=0.239;MQ=31.05;MQRankSum=1.38;QD=18.11;ReadPosRankSum=-0.431;SOR=5.889	DP:PL	1:0,3,38	.:76,6,0	0:0,0,0	.:58,0,43	1:0,3,24	4:0,12,141	0:0,0,0	1:0,3,29	.:147,0,19	.:71,0,49	5:0,0,81	1:0,0,0	0:0,0,0	6:0,18,192	.:58,6,0	1:0,3,11	1:0,0,0	0:0,0,0	.:58,0,63	0:0,0,0	4:0,12,134	3:0,0,44	3:0,9,90	0:0,0,0	0:0,0,0	0:0,0,0	2:0,6,53	.:62,0,19	3:0,9,84	2:0,6,49	.:74,0,19	1:0,3,38	2:0,0,0	0:0,0,0	2:0,6,65	0:0,0,0

Searching for genomic regions

Slicing intervals either as a contig, contig with a single position, or interval with a contig:

tachyon view -i example_dataset.yon -r "Contig110_arrow"
tachyon view -i example_dataset.yon -r "Contig110_arrow:672"
tachyon view -i example_dataset.yon -r "Contig110_arrow:672-1500"

Annotating meta-data

It is possible to annotate data with a series of INFO fields computed directly from the genotypic vectors or from the reference/alternative allele data:

Field Length Type Description
FS_A A Float PHRED-scaled Fisher's exact test P-value for allelic strand bias
AN 1 Integer Total number of alleles in called genotypes
NM 1 Integer Total number of missing alleles in called genotypes
NPM 1 Integer Total number of samples with non-reference (compared to largest) ploidy
AC A Integer Total number of alleles
AC_P A Integer Total number of alleles each strand
AF A Float Allele frequency of allele
HWE_P 1 Float Hardy-Weinberg equilibrium P-value
VT A String Variant classification (SNP, MNP, INDEL, CLUMPED, SV, UNKNOWN)
MULTI_ALLELIC 0 Flag Indicates if a site is multi-allelic (number of alternative alleles > 1)
F_PIC 1 Float Population inbreeding coefficient (F-statistic)

The contingency table, or matrix, for the Fisher's exact test (FS_A ) for strand bias looks like this:

Target allele Not target allele
Forward strand A B
Reverse strand C D

In the biallelic case, only one P-value is reported becuase of symmetry. If the site is not biallelic then each individual allele is computed separately.

Using the example dataset, we can compute those fields that are not already available by passing the flag -X

tachyon view -i example_dataset.yon -GHX

Output

Contig110_arrow	672	.	A	T	525.07	basic_filtering	AC=10;AF=0.217;AN=46;BaseQRankSum=0.967;DP=72;ExcessHet=0.8113;FS=54.73;InbreedingCoeff=-0.0525;MLEAC=11;MLEAF=0.239;MQ=31.05;MQRankSum=1.38;QD=18.11;ReadPosRankSum=-0.431;SOR=5.889;FS_A=11.5091,0;NM=26;AC_FWD=21,2;AC_REV=15,8;HWE_P=0.25072;VT=SNP