Home

Welcome to the pHASE-Stitcher wiki!

Part-A: Running phase-Stitcher

Step 01: Prepare input files.

Use the methods (Part-A: Step 01-A) from this page (https://github.com/everestial/phase-Extender/wiki/phase-Extender-Tutorial).

Step 02: Run phase-Stitcher.

Note: Parameters that are not called are set at default value.

• Call for help -

python3 phase-Stitcher.py -h

• Example 01 (trio data set) -
  assuming, ms02g sample is f1 hybrid, MA605 is mother and Sp21 is the father.

python3 phase-Stitcher.py --nt 1 --input example_01/haplotype_file01.txt --mat MA605 --pat Sp21 --f1Sample ms02g --culLH maxSum --lods 3

• Example 02 - when several samples are provided as maternal vs. paternal background.

python3 phase-Stitcher.py --nt 1 --input example_01/haplotype_file01.txt --mat MA605,MA622 --pat Sp21,Sp164 --f1Sample ms02g --outPatMatID Sp,My --culLH maxSum --lods 3

• Example 03(a) - maternal, paternal background can also be assigned by matching prefixes of several samples at once.

python3 phase-Stitcher.py --nt 1 --input example_01/haplotype_file01.txt --mat pre:MA6 --pat pre:Sp1 --f1Sample ms02g --outPatMatID Sp,My --culLH maxPd --lods 3

Code in example 03(a) will pick samples MA605,MA625 as maternal background variants and samples Sp154,Sp164 as paternal background variants. It is also possible to provide multiple comma separated prefixes to control sample assignment to particular parental background.

• Example 03(b) - with larger dataset

python3 phase-Stitcher.py --nt 1 --input example_02/haplotype_file02.txt --mat pre:MA,Nc --pat pre:Sp --f1Sample ms02g --culLH maxPd --lods 25

Code in example 03(b) will pick all Mayodan samples as maternal background variants and all Spiterstulen samples as paternal background variants.

• Example 03(c) - Use --hapStats yes to include the descriptive statistics of the final haplotype file.

python3 phase-Stitcher.py --nt 1 --input example_02/haplotype_file02.txt --mat pre:MA,Nc --pat pre:Sp --f1Sample ms02g --culLH maxPd --lods 25 --hapStats yes --outPatMatID Sp,My

Part-B: Interpreting phase-Stitcher's output

1. Interpreting data from example03 -

with script:

python3 phase-Stitcher.py --nt 1 --input example_01/haplotype_file01.txt --mat pre:MA62 --pat pre:Sp1 --f1_Sample ms02g --outPatMatID Sp,My --culLH maxSum --lods 3

Initial phase state of sample ms02g in input file is:

ms02g_PI	ms02g_PG_al
9	C|T
9	C|A
9	C|T
9	T|C
9	T|C
9	C|C
9	A|A
9	G|A
9	C|T
9	C|T

Segregated (final) phase state of sample ms02g (with computed LOD) in output files are:

## result in long format
CHROM	POS	REF	all-alleles	ms02g:PI	ms02g:PG_al	log2odds	Sp_hap	My_hap
2	14689421	T	T,C	9	C|T	6.89	C	T
2	14689451	A	A,C	9	C|A	6.89	C	A
2	14689538	T	T,C	9	C|T	6.89	C	T
2	14689544	C	C,T	9	T|C	6.89	T	C
2	14689583	C	C,T	9	T|C	6.89	T	C
2	14689641	C	C,A	9	C|C	6.89	C	C
2	14689652	A	A,T	9	A|A	6.89	A	A
2	14689658	A	A,G	9	G|A	6.89	G	A
2	14689688	T	T,C	9	C|T	6.89	C	T
2	14689691	T	T,C	9	C|T	6.89	C	T


## result in wide format
CHROM	POS_Range	ms02g:PI	hap_left	hap_right	log2odds	Sp_hap	My_hap
2	14689421-14689691	9	C-C-C-T-T-C-A-G-C-C	T-A-T-C-C-C-A-A-T-T	6.89	C-C-C-T-T-C-A-G-C-C	T-A-T-C-C-C-A-A-T-T


## statistics of the final haplotype
CHROM	phasedBlock	unphasedBlock	numVarsInPhasedBlock	numVarsInUnPhasedBlock	log2oddsInPhasedBlock	log2oddsInUnPhasedBlock	totalNumOfBlock	totalNumOfVars
2	9	.	10	.	6.89	.	1	10

What does the results tell us?

• We used maxSum as a method to estimate the likelihood and set cutoff threshold at 3 to segregate the haplotype.
• Since, the |computed lods| > lods threshold phase-Stitcher proceeds with haplotype segregation for the given RBphased haplotype.
• Since, the compute lods is a negative value, the left haplotype is assigned to paternal and right haplotype is assigned to maternal background.
• If |computed lods| < lods threshold the haplotype block won't be segregated into maternal vs. paternal background.

Note: When running recursive haplotype phase extension (in parents) the phased haplotype of F1 hybrid may now be supplied as phased reference panel.