usage: blobtools bamfilter -b FILE [-i FILE] [-e FILE] [-u] [-o PREFIX] [--sort] [--keep] [--threads INT] [-h|--help] Options: -h --help show this -b, --bam FILE BAM file (sorted by name) -i, --include FILE List of contigs whose reads are included - writes interleaved FASTQs of pairs where at least one read maps sequences in list (InUn.fq, InIn.fq, ExIn.fq) -e, --exclude FILE List of contigs whose reads are excluded (outputs reads that do not map to sequences in list) - writes interleaved FASTQs of pairs where at least one read does not maps to sequences in list (InUn.fq, InIn.fq, ExIn.fq) -u, --include_unmapped Include pairs where both reads are unmapped --sort Sort BAM file by name --keep Keep sorted BAM file (deleted otherwise) --threads INT number of sorting/compression threads for sorting [default: 2] -o, --out PREFIX Output prefix
- This script is only needed when paired-end FASTQ are to be extracted from a mapping (if single-end reads were mapped, these can easily be extracted using samtools/GNU grep).
- The module
bamfiltercan be controlled with a list of sequence IDs to include or to exclude.
- Use of an exclusion list causes all sequence IDs, except those specified, to be included
- It will output up to four interleaved FASTQ files depending on the actual mapping behaviour of the read pairs and whether the parameter
*.InIn.fqboth reads in read pair mapping to included sequences
*.InUn.fqone read mapping to an included sequence and the other being unmapped
*.ExIn.fqone read mapping to an included sequence and the other mapping to an excluded sequence
*.UnUn.fqread pairs where neither read maps to the assembly. This file is only written if
- If no exclusion/inclusion list is provided,
bamfilterwill output three interleaved FASTQ files:
- The script also writes a summary file (
*.info.txt) with the numbers of read pairs extracted for each category.
- If downstream processes require deinterleaved FASTQ files, I suggest using one of these approaches.