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
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: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
temp_files/**.sam:file
Optional intermediate SAM file
*.sam
intermediate_bam
temp_files/**.bam:file
Optional intermediate BAM file
intermediate_sorted_bam
temp_files/**.sorted.bam:file
Optional intermediate sorted BAM file
*.sorted.bam
versions
versions.yml:file
File containing software versions
versions.yml
arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
