Qploidy_par
In Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

Supported Input Types for Qploidy

VCF

Variant Call Format (VCF) files must contain genotype (GT) and allele depth (AD) fields. Qploidy extracts marker, sample, allele counts, and computes ratios. The file should have a standard VCF header, with sample columns and GT:AD values for each marker/sample.

Example (first 6 rows):

##fileformat=VCFv4.2
##source=simulated
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2
chr1 100 . A G . PASS . GT:AD 0/0:10,0 0/1:5,5
chr1 200 . T C . PASS . GT:AD 0/1:7,3 1/1:0,10
chr1 300 . G A . PASS . GT:AD 1/1:0,12 0/0:11,0
chr1 400 . C T . PASS . GT:AD 0/0:8,0 0/1:4,6
chr1 500 . A C . PASS . GT:AD 0/1:6,4 1/1:0,9

Illumina Array

Illumina array files (e.g., GSGT output) contain a header section and a [Data] section. Qploidy uses the [Data] table, which should include columns such as SNP Name, Sample ID, GC Score, Theta, X, Y, X Raw, Y Raw, and Log R Ratio. Only the [Data] section is used for analysis. Each row represents a SNP/sample combination, with X and Y as normalized intensities.

Example (first 7 rows):

[Header]
GSGT Version    2.0.5
Processing Date 4/17/2023 9:31 AM
Content         PotatoV3_20014212_A1.bpm
Num SNPs        21226
Total SNPs      21226
Num Samples     243
Total Samples   243
[Data]
SNP Name        Sample ID       GC Score        Theta   X       Y       X Raw   Y Raw   Log R Ratio
CTRL-1  AORTX07781-2    0.6814  0.247   0.023   0.009   504     100     0.5211668
CTRL-10 AORTX07781-2    0.9204  0.000   0.006   0.000   346     27      -1.021583
CTRL-100        AORTX07781-2    0.1695  0.367   0.030   0.020   576     158     1.177404
CTRL-101        AORTX07781-2    0.8655  0.222   0.026   0.010   538     102     0.3459635
CTRL-103        AORTX07781-2    0.8932  0.000   0.019   0.000   465     18      0.7578704
CTRL-104        AORTX07781-2    0.5146  0.175   0.041   0.012   675     114     1.016254
CTRL-105        AORTX07781-2    0.8060  0.450   0.018   0.015   458     132     0.4305636

Axiom Array

Axiom summary files contain several header lines, followed by a table where each marker is represented by two rows: one ending in -A (A allele) and one in -B (B allele). Columns are probeset_id and sample IDs. Each cell contains the intensity value for that allele/sample. Qploidy expects this format for conversion to long-format marker/sample tables.

Example (first 6 rows):

probeset_id sample_ID1  sample_ID2  sample_ID3
AX-86752740-A   1451.16125  1320.55213  1580.44210
AX-86752740-B   1200.55213  1100.44210  1250.16125
AX-12345678-A   1300.00000  1400.00000  1350.00000
AX-12345678-B   1100.00000  1200.00000  1150.00000
AX-87654321-A   1500.00000  1550.00000  1525.00000
AX-87654321-B   1250.00000  1300.00000  1275.00000

CSV/TSV Genotype Matrix (data)

Long format table with columns: MarkerName, SampleName, X, Y, R, ratio. Each row is a marker/sample combination, with X and Y as normalized intensities, R as total intensity, and ratio as allelic ratio.

Example (first 6 rows):

 MarkerName  SampleName  X  Y  R     ratio
1   chr1_mk1 Tetraploid1  6 27 33 0.8181818
2   chr1_mk1 Tetraploid2 36  0 36 0.0000000
3   chr1_mk1 Tetraploid3 27  7 34 0.2058824
4   chr1_mk1 Tetraploid4  0 36 36 1.0000000
5   chr1_mk1 Tetraploid5 24  8 32 0.2500000
6   chr1_mk1    Diploid1 13  8 21 0.3809524

CSV/TSV Genotype Matrix (geno)

Long format table with columns: MarkerName, SampleName, geno, prob. Each row is a marker/sample combination, with geno as genotype call and prob as confidence/probability (can be NA).

Example (first 6 rows):

  MarkerName  SampleName geno prob
1   chr1_mk1    Diploid1    1   NA
2   chr1_mk1    Diploid2    1   NA
3   chr1_mk1 Tetraploid1    3   NA
4   chr1_mk1 Tetraploid2    0   NA
5   chr1_mk1 Tetraploid3    1   NA
6   chr1_mk1 Tetraploid4    4   NA

CSV/TSV Marker Positions (geno.pos)

Table with columns: MarkerName, Chromosome, Position. Each row is a marker, with chromosome and base position.

Example (first 6 rows):

 MarkerName Chromosome Position
1   chr1_mk1       chr1  1498011
2   chr1_mk2       chr1  2548895
3   chr1_mk3       chr1  4462582
4   chr1_mk4       chr1  4832434
5   chr1_mk5       chr1  5550245
6   chr1_mk6       chr1  7873646

fitpoly File

Fitpoly output (_scores.dat) is a long format table with columns: marker, MarkerName, SampleName, ratio, P0, P1, P2, P3, P4, maxgeno, maxP, geno. Each row is a marker/sample combination, with genotype probabilities for each class, the most likely genotype, and its probability.

Example (first 6 rows): ```tsv marker MarkerName SampleName ratio P0 P1 P2 P3 P4 maxgeno maxP geno 1 AX-86752740 10049-R7P76 0.8610456158314 2.4070814263884e-165 8.85018152464261e-104 5.55270700473464e-56 3.42891056116936e-20 1 4 1 4 1 AX-86752740 195_95 0.553435636348158 5.05870449016602e-39 1.02939795506368e-12 0.999884865450636 0.000115134548334842 2.20861772506317e-35 2 0.999884865450636 2 1 AX-86752740 200_98_14 0.665553435669692 1.45062684854338e-71 1.19929721690338e-33 7.19932755628942e-10 0.999999999280061 6.3974699220722e-15 3 0.999999999280061 3 1 AX-86752740 201_98_A 0.275586122366714 0.997114692166054 0.00288530783394556 1.40533349722102e-20 5.04162645565243e-57 8.44873987719023e-129 0 0.997114692166054 0 1 AX-86752740 218_97_17 0.68427741897549 6.78529185255407e-78 5.79729809154772e-38 3.86799467535375e-12 0.999999999991422 4.70960869140837e-12