3 scripts are available with minor modifications to catch the required data in input files
- R based script with similar input file format
- VCF is converted into TSV file format with the given command below
- Convert your VCF files to TSV files before using the Rscript
Collect all your VCFs in a location for ease application of scripts
for f in *.vcf ; do cat $f | grep -v "##" | sed 's/#//g' > $f".tsv" ; done
The above is a simple for loop command used in linux terminals for keeping only required columns
3 scripts were provided, each with different set of input query format required:
- chrPos_Count.R
This script will check for Chr Pos columns in TSV files and count it for creating the output .csv file
- Catch_ChrPosRefAlt.R
This script will check for Chr-Pos and its respective Ref and Alt columns in TSV files and count it for creating the output .csv file
- Catch_ID-counter.R
This script will check for ID column in TSV files and count it for creating the output .csv file
These 3 variants of scripts required input as TSV files and query .csv file format with same headers as VCF file.
- For example: CHROM POS ID REF ALT are the available column options for query .csv file format
- Based on the Rscript variant you can use only the required columns in the input .csv file
Rscript Catch_ID-counter.R rsID-list.csv2 inputs are required for using the script
- TSV files converted from VCF file as mentioned above.
- Input .csv file any of the columns as CHROM POS ID REF ALT based on usage of script
1 output as .csv common usage format