Get short reads back from a BAM file with options for compression, splitting of forward and reverse reads, etc.
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profile-db contigs-db bin bam-file
This script get the short reads (in the form of a short-reads-fasta) out of a bam-file.
A basic run of this program is as follows:
anvi-get-short-reads-from-bam -o path/to/output \ BAM_FILE_1.bam BAM_FILE_2.bam
This will get all of the short reads out of the provided bam files (
BAM_FILE_2.bam) and put them into a single file.
You can choose to only return the short reads that are contained within a collection or bin, as so:
anvi-get-short-reads-from-bam -o path/to/output \ -c contigs-db \ -p profile-db \ -C collection \ BAM_FILE_1.bam BAM_FILE_2.bam
You can split the output based on the directionality of paired-end reads. Adding the tag
--split-R1-and-R2 causes the program to create three separate output files: one for R1 (sequences in the forward direction), one for R2 (sequences in the reverse direction; i.e. reverse complement of R1 sequences), and one for unparied reads. When doing this, you can name these three files with a prefix by using the flag
anvi-get-short-reads-from-bam -o path/to/output \ --split-R1-and-R2 \ -O BAM_1_and_BAM_2 \ BAM_FILE_1.bam BAM_FILE_2.bam
You can also compress the output by adding the flag
Edit this file to update this information.
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the
__resources__ tag in this file to see an example.