Description

QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bams (file)

(Mandatory) BAM/CRAM files

*.{bam,cram,sam}

bais (file)

(Mandatory) BAM/CRAM index files

*.{bai}

reference_haplotype_file (file)

(Mandatory) Reference haplotype file in IMPUTE format (file with no header and no rownames, one row per SNP, one column per reference haplotype, space separated, values must be 0 or 1)

*.{hap.gz}

reference_legend_file (file)

(Mandatory) Reference haplotype legend file in IMPUTE format (file with one row per SNP, and a header including position for the physical position in 1 based coordinates, a0 for the reference allele, and a1 for the alternate allele).

*.{legend.gz}

chr (string)

(Mandatory) What chromosome to run. Should match BAM headers.

regions_start (integer)

(Mandatory) When running imputation, where to start from. The 1-based position x is kept if regionStart <= x <= regionEnd.

regions_end (integer)

(Mandatory) When running imputation, where to stop.

buffer (integer)

Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd.

ngen (integer)

Number of generations since founding or mixing. Note that the algorithm is relatively robust to this. Use nGen = 4 *.Ne / K if unsure.

genetic_map_file (file)

(Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate).

*.{txt.gz}

meta2 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

posfile (file)

(Optional) File with positions of where to impute, lining up one-to-one with genfile. File is tab seperated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized.

*.{txt}

phasefile (file)

(Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab seperated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header.

*.{txt}

meta3 (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

(Optional) File with reference genome.

*.{txt.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

vcf (file)

VCF file with both SNP annotation information and per-sample genotype information.

*.{vcf.gz}

tbi (file)

TBI file of the VCF.

*.{vcf.gz.tbi}

rdata (directory)

Optional directory path to prepared RData file with reference objects (useful with —save_prepared_reference=TRUE).

plots (directory)

Optional directory path to save plots.

Tools

quilt
GPL v3

Read aware low coverage whole genome sequence imputation from a reference panel