anvi-get-short-reads-from-bam [program]
Table of Contents
Get short reads back from a BAM file with options for compression, splitting of forward and reverse reads, etc.
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Can provide
Can consume
profile-db 
contigs-db bin 
bam-file 
Usage
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_1.bam and BAM_FILE_2.bam) and put them into a single file.
Narrowing the input
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
Changing the output format
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 -O.
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 --gzip-output
Edit this file to update this information.
Additional Resources
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.