Description

Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.

Input

name:type
description
pattern

meta:map

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

]

bam:file

BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads.

*.bam

Output

name:type
description
pattern

extracted_reads_fastq

meta:map

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

]

*.fq.gz:file

FASTQ file(s) containing chromosome 6 reads and related HLA sequences

*.fq.gz

log

*.log:file

Log file for run summary

*.log

intermediate_sam

meta:map

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

]

temp_files/**.sam:file

Optional intermediate SAM file

*.sam

intermediate_bam

meta:map

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

]

temp_files/**.bam:file

Optional intermediate BAM file

*.bam

intermediate_sorted_bam

meta:map

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

]

temp_files/**.sorted.bam:file

Optional intermediate sorted BAM file

*.sorted.bam

versions

versions.yml:file

File containing software versions

versions.yml

Tools

arcashla
GPL v3

arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.