PTAS (Prenatal paternity Test Analysis System）provides a novel CPI and CPE models specifically for non-invasive prenatal paternity testing (NIPPT). Users can upload sequencing data of alleged father genomic DNA, mother gDNA and mother cfDNA. Unique molecular identifiers (UMI) is also supported to reduce sequencing errors in early pregnancy samples.
tar -xvf PTAS.tar.gz
cd ./PTAS
make install
Dependancies installed by Makefile:
And various perl modules.
Please see the respective licence for each before use.
For paired-end sequencing:
perl ptas.pl --snp SNPLIST --f1 FASTQ1 --f2 FASTQ2 --m1 FASTQ1 --m2 FASTQ2 --c1 FASTQ1 --c2 FASTQ2 --w 6 [options]
For single-end sequencing:
perl ptas.pl --snp SNPLIST --f1 FASTQ1 --m1 FASTQ1 --c1 FASTQ1 --w 6 [options]
The options are:
| Option | Effect |
|---|---|
| f1 | .fastq file 1 of father (Required) |
| f2 | .fastq file 2 of father |
| m1 | .fastq file 1 of mather (Required) |
| m2 | .fastq file 1 of mather |
| c1 | .fastq file 1 of child (Required) |
| c2 | .fastq file 1 of child |
| snp | A list of snp for paternity test (Required) |
| w | gestational weeks. Default is 8. (If not set, the two critical points of MBF will be set to 0.001 and 0.01) |
| out | Output Directory (Required) |
| n | Threads number. Default is 4. |
| r | Same as --read-structure in fgbio ExtractUmisFromBam. '3M2S+T,3M2S+T' is set as default. |
| t | Same as --molecular-index-tags in fgbio ExtractUmisFromBam. 'ZA,ZB' is set as default. |
| umi | enable the unique molecular identifier sequences analysis |
| sur | enable the paternity analysis for surrogacy duo cases (conflicts with --umi) |
A SNP list is required for the generation and alignment of upstream and downstream sequences. If you need to customize the SNP panel, you need to refer to PTAS/db/nipptRESHAPE.tsv and PTAS/ref/nipptRESHAPE.hg19.fa to modify the database. Below is an example of a tsv file:
| SNPid | Chr.hg19 | Pos.hg19 | Chr.GRCh38 | Pos.GRCh38 | Alleles with Frequency |
|---|---|---|---|---|---|
| rs75062661 | chr1 | 69511 | - | - | A |
| rs77418980 | chr1 | 91536 | - | - | G |
| rs151118460 | chr1 | 91581 | - | - | G |
| rs4951859 | chr1 | 729679 | - | - | C |
| rs143214544 | chr1 | 748878 | - | - | G |
Where location information is not necessary.
In addition, the reference sequence should ensure that the SNP locus is located at position 501.