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

meta (map)

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

]

extracted_reads_fastq (file)

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

*.fq.gz

log (file)

Log file for run summary

*.log

intermediate_sam (file)

Optional intermediate SAM file

*.sam

intermediate_bam (file)

Optional intermediate BAM file

*.bam

intermediate_sorted_bam (file)

Optional intermediate sorted BAM file

*.sorted.bam

versions (file)

File containing software versions

versions.yml
author
Github user christopher-mohr
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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.

github.com/RabadanLab/arcasHLA 10.1093/bioinformatics/btz474