Quality Check¶
qcVCF¶
qcVCF produces a report in JSON format with different quality metrics calculated for input VCF file. Both single sample and family-based metrics are available.
Arguments¶
usage: granite qcVCF [-h] -i INPUTFILE -o OUTPUTFILE -p PEDIGREE --samples
SAMPLES [SAMPLES ...] [--ti_tv] [--trio_errors]
[--het_hom]
optional arguments:
-i INPUTFILE, --inputfile INPUTFILE
input VCF file
-o OUTPUTFILE, --outputfile OUTPUTFILE
output file to write results as JSON, use .json as
extension
-p PEDIGREE, --pedigree PEDIGREE
pedigree information, either as JSON file or JSON
representation as string
--samples SAMPLES [SAMPLES ...]
list of sample IDs to get stats for (e.g. --samples
SampleID_1 [SampleID_2] ...)
--ti_tv add transition-transversion ratio and statistics on
substitutions to report
--trio_errors add statistics on mendelian errors based on trio to
report
--het_hom add heterozygosity ratio and statistics on zygosity to
report
validateVCF¶
validateVCF produces a report in JSON format with error models for different inheritance modes calculated for input VCF file. Additional supporting plots are generated in PNG format.
Arguments¶
usage: granite validateVCF [-h] -i INPUTFILE -o OUTPUTFILE -p PEDIGREE
[PEDIGREE ...] --anchor ANCHOR [ANCHOR ...]
[--het HET [HET ...]] [--novo NOVO] [--verbose]
optional arguments:
-i INPUTFILE, --inputfile INPUTFILE
input VCF file
-o OUTPUTFILE, --outputfile OUTPUTFILE
output file to write results as JSON, use .json as
extension
-p PEDIGREE [PEDIGREE ...], --pedigree PEDIGREE [PEDIGREE ...]
pedigree information, either as JSON file or JSON
representation as string. It is possible to specify
multiple pedigrees to load as list (e.g. --pedigree
pedigree_1 [pedigree_2] ...)
--anchor ANCHOR [ANCHOR ...]
sample ID to be used as anchor in pedigree to build
family. It is possible to specify multiple sample IDs
as list. If multiple pedigrees are specified in "--
pedigree", anchors are positionally matched to
corresponding pedigree
--het HET [HET ...] sample ID to be used to calculate error model for
heterozygous mutations. It is possible to specify
multiple sample IDs as list. Each sample ID must
correspond to anchor specified in "--anchor"
--novo NOVO sample ID to be used to calculate error model for de
novo mutations. Must correspond to anchor specified in
"--anchor". Requires posterior probability from
novoCaller
--type TYPE [TYPE ...]
by default error models are calculated only for SNV.
It is possible to specify different types of variant
to use (SNV, INS, DEL, MNV, MAV) as list (e.g. --type
SNV INS DEL)
SVqcVCF¶
SVqcVCF produces a report in JSON format with different quality metrics calculated for input SV VCF file. Currently, this function can count DEL and DUP SVs in single- and multi-sample SV VCF files. It reports the number of DEL, DUP, and total (the sum of only DEL and DUP) SVs for each sample provided in samples. Other SVTYPEs (INS, INV, CNV, BND) are currently ignored.
Arguments¶
usage: granite SVqcVCF [-h] -i INPUTFILE -o OUTPUTFILE
--samples SAMPLES [SAMPLES ...] [--verbose]
optional arguments:
-i INPUTFILE, --inputfile INPUTFILE
input SV VCF file
-o OUTPUTFILE, --outputfile OUTPUTFILE
output file to write results as JSON, use .json as
extension
--samples SAMPLES [SAMPLES ...]
list of sample IDs to get stats for (e.g. --samples
SampleID_1 [SampleID_2] ...)