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Reference Flow parameters

Data-dependent parameters

For users interested in the default RandFlow-LD pipeline based on GRCh38 and 1KG GRCh38 call set, changing parameters in this section is sufficient.

  • READS1 : reads to align

  • INDIV : name of the tested sample. This parameter is used to name directories and files.

  • DIR : directory where the outputs will be put

  • THREADS : max number of threads used for each rule. This is different from the number specified by snakemake -j <t>, which is the number of threads for the entire Snakemake pipeline. I.e., there can be multiple programs running with THREADS until the sum reaches <t>.

Pipeline options

  • USE_PREBUILT : whether to use the RandFlow-LD pre-built indexes

  • SORT_SAM : whether to sort the final SAM output

  • ALN_MAPQ_THRSD : mapping quality cutoff to split read into committed and deferred groups

Dataset parameters

  • GENOME : reference genome; usually a standard GRC genome

  • DIR_VCF : directory where the VCFs are put

  • VCF_PREFIX, VCF_SUFFIX : prefix and suffix of a VCF file. For example, we set VCF_PREFIX to "ALL.chr" and VCF_SUFFIX to ".shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz" for the 1KG GRCh38 call set, where the VCFs are named as "ALL.chr.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz"

  • CHROM : a list specifying chromosomes included. Reference flow finds VCFs corresponding to the specified chromosomes and builds population genomes for them.

  • GROUP : population groups included to build second pass population genomes

Second-pass genome parameters

  • POP_THRSD : allele frequency threshold. 0: do not filter by frequency; 0.5: only use major alleles

  • POP_STOCHASTIC : whether to use stochastic update. 1: stochastic update; 0: deterministic

  • POP_BLOCK_SIZE : size of phase-preserving LD blocks. Set to 1 when doing independent sampling. Only applicable to call sets providing phase information.

  • POP_USE_LD : whether to include local LD information. 1: phase-preserving; 0: independent-sampling

We provided configurations for MajorFlow, RandFlow and RandFlow-LD in the file. Users may uncomment the setting of interest.

Individual-population mappings

  • FAMILY : mapping between individuals and populations
  • SPOP : mapping between populations and super populations

Currently we only support call sets from the 1000 Genomes Project, including phase-3 and GRCh38 call sets. Default mappings are provided under ../resources directory. For users interested in using other call sets, changes in the pipeline may be needed depending on the labelling and VCF format adopted by the call set. FAMILY and SPOP are used under the prepare_pop_indiv rule in shared/prepare_pop_genome.Snakefile and the build_dict_pop_to_spop rule in shared/functions.Snakefile.

Chromosomal mappings

  • LENGTH_MAP : lengths for each chromosome
  • CHROM_MAP : mapping from 1 to chr1, etc

Paths of software

  • BCFTOOLS : we used bcftools 1.9-206-g4694164. There is a bcftools consensus issue with the major release so we used a development version.

  • SAMTOOLS : we used samtools v1.9

  • LIFTOVER : ../liftover/liftover

  • PYTHON: we developed Reference flow using Python3.7

  • DIR_SCRIPTS : ../src

Randomness control

  • RAND_SEED: random seed used in the reference flow stochastic reference genome update process and for aligner