Description

Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites.

Input

name:type
description
pattern

meta{:bash}

:file

Input SAM/BAM/CRAM file

bam{:bash}

:file

BAM file

*.{bam}

bai{:bash}

:file

BAM index file

*.{bai}

haplotype_map{:bash}

:file

A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.

*.{txt,vcf,vcf.gz}

fasta{:bash}

:file

Reference sequence file

*.{fasta,fna,fa}

fasta_fai{:bash}

:file

Reference sequence index file

*.{fai}

sequence_dictionary{:bash}

:file

Reference sequence dictionary file

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.vcf.gz{:bash}

:file

VCF file

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.vcf.gz.tbi{:bash}

:file

Tabix index file

*.vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

broadinstitute.github.io/picard https://github.com/broadinstitute/picard/
maintainers
Github user adamrtalbot
Github user mauro-saporita
get in touch
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