vcHMM

Implementation of Hidden Markov Model (Viterbi) algorithm for the identification of sequence variants.

Milestone Chart

Milestone	Scheduled Beginn	Scheduled Completion

Project Plan	13.11.2019	20.11.2019
Data Management Plan	13.11.2019	20.11.2019
Data acquisition	20.11.2019	24.11.2019
Working algorithm	25.11.2019	20.12.2019
transition matrix
update ref and sam
emission matrix
HMM viterbi
Comparison with other tools	21.12.2019	29.12.2019
Report	06.01.2020	11.01.2020
Hand in		12.01.2020
Presentation		20.01.2020

General info
ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/

Data that we need:
ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/CompleteGenomics_normal/BAM/

Reference Sequences:
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
Additional information: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Name		Name	Last commit message	Last commit date
Latest commit History 144 Commits
data		data
.DS_Store		.DS_Store
10X_Coverage_sort		10X_Coverage_sort
10x_cov_read1.vcf		10x_cov_read1.vcf
30x_cov_read1.vcf		30x_cov_read1.vcf
30x_evaluation_example.vcf		30x_evaluation_example.vcf
README.md		README.md
Sequence_Project_tmatrix.txt		Sequence_Project_tmatrix.txt
Simulated_Data_TempData.7z		Simulated_Data_TempData.7z
Simulated_Data_TempData_2.7z		Simulated_Data_TempData_2.7z
Trans Matrix		Trans Matrix
emission-matrix.py		emission-matrix.py
eval_matlab_10x.txt		eval_matlab_10x.txt
evaluation.txt		evaluation.txt
evaluation_10x_read1.txt		evaluation_10x_read1.txt
evaluation_30x_read1.txt		evaluation_30x_read1.txt
example.vcf		example.vcf
example_30x_coverage.vcf		example_30x_coverage.vcf
finalout.vcf		finalout.vcf
find_base_state.py		find_base_state.py
get_sam_reads.py		get_sam_reads.py
new_alignment_test.txt		new_alignment_test.txt
output_new.vcf		output_new.vcf
output_new1.vcf		output_new1.vcf
output_wo_HandS.vcf		output_wo_HandS.vcf
outstat.txt		outstat.txt
outstat_HS.txt		outstat_HS.txt
outstat_SandH.txt		outstat_SandH.txt
ref.fa		ref.fa
runHMMvar.m		runHMMvar.m
test_file.txt		test_file.txt
toVictoryAndBeyond.sh		toVictoryAndBeyond.sh
variant_calling_output.py		variant_calling_output.py
vcHMM.py		vcHMM.py
vcHMM1.vcf		vcHMM1.vcf
vcHMMfinal.py		vcHMMfinal.py
vi-HMM-master_runBoyRun.7z		vi-HMM-master_runBoyRun.7z
viHMMV1.py		viHMMV1.py
vi_hmm.py		vi_hmm.py
viterbi.py		viterbi.py