Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads.
*.bam
extracted_reads_fastq
*.fq.gz
FASTQ file(s) containing chromosome 6 reads and related HLA sequences
log
*.log
Log file for run summary
intermediate_sam
temp_files/**.sam
Optional intermediate SAM file
*.sam
intermediate_bam
temp_files/**.bam
Optional intermediate BAM file
intermediate_sorted_bam
temp_files/**.sorted.bam
Optional intermediate sorted BAM file
*.sorted.bam
versions_arcashla
${task.process}
:string
The name of the process
arcashla
The name of the tool
0.5.0
The version of the tool
versions
arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
