Commands reference

From PileLine

Processing and Annotation Commands

• pileline-fastseek.sh

Prints a given range of a locus file:

pileline-fastseek.sh –p <locus_file.txt> -s chr10:100:10000

• pileline-fastsjoin.sh

Joins two positional files:

XXXXX

• pileline-rfilter.sh

Filters (or annotates) a positional file with range-based annotations (in bed format). Each position that is inside of a specific range is annotated.

pileline-rfilter –A <locus_file.txt> –i <targets.bed> –o <out.txt>
pileline-rfilter --annotate –A <locus_file.tx> –i <annotations.bed> –o <out.txt>

• pileline-genindex.sh

Indexes fasta genome and then can perform range based queries in that genome.

pileline-genindex –-index –g <fasta> -i <new_index>
pileline-genindex --seek –i <index> -s chr1:1000:2000

• pileline-pileup2sift.sh

Generates a SIFT-compatible change column for each variant line in the GPF.

pileline-pileup2sift -i <pileup> 
#Use - for STDIN.

• pileline-pileup2polyphen.sh

Generates a Polyhen-compatible change column for each variant line in the GPF.

pileline-pileup2polyphen -i <pileup> 
#Use - for STDIN.

Analysis Commands

• pileline-2smc.sh

Looks for discrepancies in genotypes of two samples (i.e.: case vs control). It also can annotate each output position with a given positional file containing custom annotations (i.e. dbSNP). Also produces a SIFT and PolyPhen-2 compatible outfiles.

• pileline-nsmc.sh

Takes the output of several 2smc comparisons commands to reports where variants are reproduced.

• pileline-genotest.sh

Calculates the NGS performance on genotyping, surveying a set of genomic positions whose genotype is known in the sample.