Utilities¶
mpileupCounts¶
mpileupCounts uses samtools to access input BAM and calculates statistics for reads pileup at each position in the specified region, returns counts in RCK format.
Arguments¶
usage: granite mpileupCounts [-h] -i INPUTFILE -o OUTPUTFILE -r REFERENCE
[--region REGION] [--MQthr MQTHR] [--BQthr BQTHR]
optional arguments:
-i INPUTFILE, --inputfile INPUTFILE
input file in BAM format
-o OUTPUTFILE, --outputfile OUTPUTFILE
output file to write results as RCK format (TSV), use
.rck as extension
-r REFERENCE, --reference REFERENCE
reference file in FASTA format
--region REGION region to be analyzed [e.g. chr1:1-10000000,
1:1-10000000, chr1, 1], chromosome name must match the
reference
--MQthr MQTHR minimum mapping quality for an alignment to be used
(>=) [0]
--BQthr BQTHR minimum base quality for a base to be considered (>=)
[13]
toBig¶
toBig converts counts from bgzip and tabix indexed RCK format into BIG format. Positions are “called” by read counts or allelic balance for single or multiple files (joint calls) in specified regions. Positions “called” are set to True (or 1) in BIG binary structure.
Arguments¶
usage: granite toBig [-h] [-i INPUTFILE [INPUTFILE ...]] -o OUTPUTFILE -r
REGIONFILE -f CHROMFILE [--ncores NCORES] --fithr FITHR
[--rdthr RDTHR] [--abthr ABTHR]
optional arguments:
-f FILE, --file FILE file to be used to call positions. To do joint calling
specify multiple files as: "-f file_1 -f file_2 -f ...".
Expected bgzip and tabix indexed RCK file
-o OUTPUTFILE, --outputfile OUTPUTFILE
output file to write results as BIG format (binary
hdf5), use .big as extension
-r REGIONFILE, --regionfile REGIONFILE
file containing regions to be used [e.g.
chr1:1-10000000, 1:1-10000000, chr1, 1] listed as a
column, chromosomes names must match the reference
-c CHROMFILE, --chromfile CHROMFILE
chrom.sizes file containing chromosomes size
information
--ncores NCORES number of cores to be used if multiple regions are
specified [1]
--fithr FITHR minimum number of files with at least "--rdthr" for
the alternate allele or having the variant, "calls" by
allelic balance, to jointly "call" position (>=)
--rdthr RDTHR minimum number of alternate reads to count the file in
"--fithr", if not specified "calls" are made by
allelic balance (>=)
--abthr ABTHR minimum percentage of alternate reads compared to
reference reads to count the file in "--fithr" when
"calling" by allelic balance (>=) [15]
Examples¶
toBig can be used to calculate positions to blacklist for common variants by using unrelated samples. This command will set to True in BIG structure positions with allelic balance for alternate allele equal/higher than --abthr in more that --fithr samples (joint calling).
granite toBig -f file -f file -f file -f file -f ... -o file.out.big -c file.chrom.sizes -r file.regions --fithr <int> --abthr <int>
Absolute reads count can be used instead of allelic balance to call positions. This command will set to True in BIG structure positions with reads count for alternate allele equal/higher than --rdthr in more that --fithr samples (joint calling).
granite toBig -f file -f file -f file -f file -f ... -o file.out.big -c file.chrom.sizes -r file.regions --fithr <int> --rdthr <int>
rckTar¶
rckTar creates a tar archive from bgzip and tabix indexed RCK files. Creates an index file for the archive.
Arguments¶
usage: granite rckTar [-h] -t TTAR -f FILE
optional arguments:
-t TTAR, --ttar TTAR target tar to write results, use .rck.tar as extension
-f FILE, --file FILE file to be archived. Specify multiple files as: "-f
SampleID_1.rck.gz -f SampleID_2.rck.gz -f ...". Files
order is maintained while creating the index