updated readme

README.md

@@ -2,7 +2,7 @@
 Population genomics from metagenomes
 
 ### Description
-POGENOM takes as input a file of the variant call format (VCF). This is generated by mapping one or several metagenome samples against a reference genome with a read aligner and calling variants using a variant caller. POGENOM calculates the nucleotide diversity (𝛑) within each sample. If a multiple sample vcf file is provided as input, the fixation index (FST) will also be calculated between each pair of samples. If, in addition to the VCF file, an annotation file of the General Feature Format (GFF) is provided as input, gene-wise 𝛑 and FST will also be calculated. If further a genetic code file is provided, gene-wise 𝛑 and FST will be calculated also at the amino acid level. Now also non-synonymous to synonymous polymorphism rates (pN/pS) will be calculated for each gene in each sample. POGENOM also calculates some of the above parameters for all samples collectively, treating them as a metasample.
+POGENOM takes as input a file of the variant call format (VCF). This is generated by mapping one or several metagenome samples against a reference genome with a read aligner and calling variants using a variant caller. POGENOM calculates the nucleotide diversity (𝛑) within each sample. If a multiple-sample vcf file is provided as input, the fixation index (FST) will also be calculated between each pair of samples. If, in addition to the VCF file, an annotation file of the General Feature Format (GFF) is provided as input, gene-wise 𝛑 and FST will also be calculated. If, further, a genetic code file is provided, gene-wise 𝛑 and FST will be calculated also at the amino acid level. Now also non-synonymous to synonymous polymorphism rates (pN/pS) will be calculated for each gene in each sample. POGENOM also calculates some of the above parameters for all samples collectively, treating them as a metasample. For gene- and loci-wise calculations, a genome sequence needs to be provided. This can either be included in the end of the GFF file (in fasta version) or be provided as a separate fasta file. 
 
 ----
 
@@ -21,6 +21,9 @@ Or:
 
 `perl pogenom.pl -vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --gff_file GFF_FILE [--help]`
 
+Or:
+
+`perl pogenom.pl -vcf_file VCF_FILE --out OUTPUT_FILES_PREFIX --fasta_file FASTA_FILE [--help]`
 
 
 ### Required arguments
@@ -29,26 +32,29 @@ Or:
 
 `--out OUTPUT_FILES_PREFIX`             Specify the prefix of the output file name(s) (overwrites existing files with same names).
 
-`--genome_size GENOME_SIZE`             Specify genome size (in bp; integer). Not required if `--gff_file` is given.
+`--genome_size GENOME_SIZE`             Specify genome size (in bp; integer). Not required if `--gff_file` or `--fasta_file` with genome sequence is given.
 
 
 
 ### Optional arguments
 
-`--gff_file GFF_FILE`                   Specify gff file. Either this or `--genome_size` must be given.
+`--gff_file GFF_FILE`                   Specify gff file. Either this, `--genome_size` or `--fasta_file` must be given.
+
+`--fasta_file FASTA_FILE`               Specify fasta file. Either this, `--genome_size` or `--gff_file` must be given
 
 `--genetic_code_file GENETIC_CODE_FILE` Specify genetic code file. E.g. `standard_genetic_code.txt` in the POGENOM distribution.
 
-`--loci_file LOCI_FILE`                 Specify file with ids for loci to include.
+`--loci_file LOCI_FILE`                 Specify file with ids of loci to include.
 
 `--min_count MIN_COUNT`                 Specify minimum coverage for a locus to be included for the sample.
 
-`--min_found MIN_FOUND_IN`              Specify minimum number samples that a locus need to be present in to be included.
+`--min_found MIN_FOUND_IN`              Specify minimum number samples that a locus needs to be present in to be included.
 
 `--subsample SUBSAMPLE`                 Specify coverage level at which to subsample.
 
 `--keep_haplotypes`                     If this is used, POGENOM will not split haplotypes into single-nucleotide variants, which is otherwise the default behaviour.
-`--vcf_version`                         Specify VCF file format version. Can be set to 4.2 or 4.1 (default).
+
+`--vcf_format`                          Specify VCF file format version. Can be set to freebayes (default) or GATK.
 
 `--help`                                To print help message on screen.