bamfilter
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
Comments
- 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
bamfilter
can 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
--include_unmapped
is provided: *.InIn.fq
both reads in read pair mapping to included sequences*.InUn.fq
one read mapping to an included sequence and the other being unmapped*.ExIn.fq
one read mapping to an included sequence and the other mapping to an excluded sequence*.UnUn.fq
read pairs where neither read maps to the assembly. This file is only written if--include_unmapped
is provided- If no exclusion/inclusion list is provided,
bamfilter
will output three interleaved FASTQ files: *.InIn.fq
*.InUn.fq
*.UnUn.fq
- 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.
Updated about 7 years ago