diff --git a/README.md b/README.md
index 53108f9..0f27200 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,11 @@
# VCF-Simplify v2.1
-A python parser to simplify the vcf file into table like format.
-There are several tools available to mainpulate and alter VCF file.
-But, a simple and comprehensive tool that can produce a most simple
-output required by emperical biologist is still amiss.
+A python parser to simplify the vcf file into a (pseudo-)tabular format.
+There are several tools available to mainpulate and alter VCF files.
+But, a simple but expansive tool that can produce most simple
+output is required by empirical biologist is still amiss.
- **Convert VCF to TABLE**\
- This tool takes in sorted vcf file and reports a simplified table output
+ This tool takes in a sorted vcf file and reports a simplified tabular output
for `INFO` and `FORMAT` field for each `SAMPLE` of interest. With default
state (minimal code) all the `INFO`, `FORMAT` for all the `SAMPLE` are
simplified. Fields can be further narrowed down using very convenient
@@ -17,15 +17,10 @@ and comprehensive scripts.
-**Exclusively for [phase-Stitcher](https://github.com/everestial/pHASE-Stitcher) and [phase-Extender](https://github.com/everestial/phase-Extender).**
+**Exclusively for [phase-Stitcher](https://github.com/everestial/pHASE-Stitcher) and [phase-Extender](https://github.com/everestial/phase-Extender).** Controlled workflows are included.
- **Convert VCF to Haplotype**\
- It is also possible to convert the TABLE file into VCF. Controlled,
- workflows are included.
-
- **Convert Haplotype to VCF**\
- It is also possible to convert the TABLE file into VCF. Controlled,
- workflows are included.
-
+
## Prerequisites :
@@ -95,12 +90,12 @@ optional arguments:
Additional flags for "VCF To Haplotype":
-PG PG FORMAT tag containing the phased genotype of the
- SAMPLE. Only applicable on 'haplotype file output'.
+ SAMPLE. Only applicable for 'haplotype file output'.
-PI PI FORMAT tag representing the unique index of RBphased
- haplotype block in the SAMPLE. Only applicable on
+ haplotype block in the SAMPLE. Only applicable for
'haplotype file output'. Note: 'CHROM' can also be
used as PI if VCF is phased chromosome-wide.
- -unphased UNPHASED include unphased variants in the output. Aavailable
+ -unphased UNPHASED include unphased variants in the output. Available
options: yes, no
Additional flags for "VCF To Table":
@@ -264,10 +259,10 @@ usage: VCF-Simplify BuildVCF [-h] -fromType FROMTYPE -inFile INFILE -outVCF
optional arguments:
-h, --help show this help message and exit
- -fromType FROMTYPE Type of the input file the VCF is being prepared from.
+ -fromType FROMTYPE Type of the input file to prepare the VCF from.
Options: haplotype, table
- -inFile INFILE Sorted table or haplotype file.This haplotype file
- should be obtained from phase-Stitcher, phase-
+ -inFile INFILE Sorted table or haplotype file. This haplotype file
+ can be obtained from phase-Stitcher or phase-
Extender. The table file should be in the format
output by 'VCF-Simplify'; only long format table is
supported for now.
diff --git a/VCF-Simplify.py b/VCF-Simplify.py
index 583d27b..9d2b8f9 100644
--- a/VCF-Simplify.py
+++ b/VCF-Simplify.py
@@ -81,20 +81,20 @@ def main():
"Options: no(0), yes(1). Default: 0 .",
required=False, default=0)
- '''Task-B: Sub parser for "BuildVCF". To create VCF from simple Table like format. '''
+ '''Task-B: Sub parser for "BuildVCF". To create VCF from a tabular format. '''
parser_b = subparsers.add_parser('BuildVCF',
help='Create VCF : from a haplotype or a table file. ')
# upper level parser within BuildVCF
''' Task - B(01) : From Haplotype To VCF - only require these arguments. '''
parser_b.add_argument("-fromType", required=True,
- help="Type of the input file the VCF is being prepared from. "
+ help="Type of the input file to prepare the VCF. "
"Options: haplotype, table ")
parser_b.add_argument("-inFile", required=True,
help="Sorted table or haplotype file."
- "This haplotype file should be obtained from phase-Stitcher, "
+ "This haplotype file can be obtained from phase-Stitcher or "
"phase-Extender. The table file should be in the format "
- "output by 'VCF-Simplify'; only long format table is supported for now.")
+ "output by 'VCF-Simplify'; only long format table is currently supported.")
parser_b.add_argument("-outVCF", help="Name of the output VCF file.", required=True)
parser_b.add_argument("-vcfHeader", required=True,