[options] parsnip path_to_ref/ucsc.hg19.fasta output-path/out-prefix output_vcf_path/vcfFileNamePrefix`
The first non-optional argument is the reference fasta file. The second non-optional argument is the same as SAMPA's second argument and the third non-optional argument is the prefix for the output vcf file to be created (.vcf is added to this argument).
PARSNIP's optional arguments are described below.
-t INT number of threads [Default value: 1]
--MQ=INT minimum average SNP mapping quality filter [Default value: 20]. This is the average mapping quality of the reads which have an alternate allele occuring at this position.
--DP=INT minimum read depth filter [Default value: 2]. Total read depth at this position.
--SB=REAL minimum strand bias filter [Default value: .1]. This filter reduces false positive SNP calls by eliminating SNPs which occur primarily on either forward or reverse strands. SB=0 indicates that SNPs occur wholly in one type of strand (False positive) and SB=1 indicates that SNP occurs in both strand types in equal proportions.
--AAF=INT minimum alternate allele frequency filter [Default value: 20]. Denotes the percentage of reads with alternate allele among all reads mapping to this position.
--AAC=INT minimum alternate allele count filter [Default value: 2]. This is the number of occurences of the alternate allele.
We have tested SPRITE on the data sets provided by the
[SMASH](http://smash.cs.berkeley.edu) genetic variant benchmarking
toolkit and Platinum Genomes NA12878 and NA12877 provided by [Illumina](http://www.illumina.com/platinumgenomes/).
### Assumptions and Limitations
* Both read files of a sample in case of paired-end reads are assumed to have the same read length.
* We have tested SPRITE only for Illumina sequenced reads.
* The FASTQ files should be uncompressed before generating FASTQ index file using prune-genreadidx program.
* PRUNE does not perform I/O concurrently with alignment.
### Support, Comments, Suggestions
Please email Vasudevan Rengasamy (