Usage

get_mnv [OPTIONS] --vcf <VCF_FILE> --fasta <FASTA_FILE> --genes <GENES_FILE>

Options:

• -v, --vcf <VCF_FILE>: VCF file containing the SNVs. (Required)
• -b, --bam <BAM_FILE>: BAM file with aligned reads. (Optional)
• -f, --fasta <FASTA_FILE>: FASTA file with the reference sequence. (Required)
• -g, --genes <GENES_FILE>: File containing gene information. (Required)
• -q, --quality : Minimum Phred quality score (default: 20).

Example:

get_mnv \
  --vcf variants.vcf \
  --bam reads.bam \
  --fasta reference.fasta \
  --genes genes.txt \
  --quality 30

Input File Formats

• VCF File: Should contain the identified SNVs.
• BAM File: (Optional) Genomic reads aligned to the reference sequence.
• FASTA File: Reference genomic sequence.
• Gene File: A tab-delimited text file with the following structure per line (GeneName,GeneStart,GeneEnd,Strand):

Rv0007_Rv0007	9914	10828	+
ileT_Rvnt01	10887	10960	+
alaT_Rvnt02	11112	11184	+
Rv0008c_Rv0008c	11874	12311	-
ppiA_Rv0009	12468	13016	+
Rv0010c_Rv0010c	13133	13558	-

Output

The program generates a TSV file named <vcf_filename>.MNV.tsv containing the following information:

• Gene: Name of the gene.
• Positions: Positions of the variants.
• Base Changes: Nucleotide base changes.
• AA Changes: Resulting amino acid changes.
• SNP AA Changes: Amino acid changes if considering individual SNVs.
• Variant Type: Type of variant (SNP, MNV, or SNP/MNV).
• Change Type: Type of change at the protein level (Synonymous, Non-synonymous, Stop gained).
• SNP Reads: (If BAM provided) Count of reads supporting each SNP.
• MNV Reads: (If BAM provided) Count of reads supporting the MNV.

Example:

Gene	Positions	Base Changes	AA Changes	SNP AA Changes	Variant Type	Change Type	SNP Reads	MNV Reads
Rv0095c_Rv0095c	104838	T	Asp126Glu	Asp126Glu	SNP	Non-synonymous	0	16
Rv0095c_Rv0095c	104941,104942	T,G	Gly92Gln	Gly92Glu; Gly92Arg	MNV	Non-synonymous	0,0	25
esxL_Rv1198	1341044	C	His13His	His13His	SNP	Synonymous	0	41
esxL_Rv1198	1341083	G	Ala26Ala	Ala26Ala	SNP	Synonymous	0	12
esxL_Rv1198	1341102,1341103	T,C	Arg33Ser	Arg33Cys; Arg33Pro	MNV	Non-synonymous	0,0	11