Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Can you add sort by tag function? #499

Open
cherryamme opened this issue Dec 13, 2022 · 1 comment
Open

Can you add sort by tag function? #499

cherryamme opened this issue Dec 13, 2022 · 1 comment
Labels
Follow the checklist to report an issue Did you follow the https://github.com/biod/sambamba#check-list ?

Comments

@cherryamme
Copy link

hi, there is a '-t' arg in sammtools to Sort by value of TAG. but i can't find alternative arg in sambamba .
I've seen some closed issue #309 in 2017 also Mentioned. but there is no solution .
How can i sort by value of tag.

@pjotrp pjotrp added the Follow the checklist to report an issue Did you follow the https://github.com/biod/sambamba#check-list ? label Dec 18, 2022
@cherryamme
Copy link
Author

I have tried the latest release of Sambamba 0.8.2

sambamba 0.8.2
by Artem Tarasov and Pjotr Prins (C) 2012-2021
LDC 1.27.1 / DMD v2.097.2 / LLVM11.0.0 / bootstrap LDC - the LLVM D compiler (1.27.1)

Usage: sambamba-sort [options] <input.bam>

Options: -m, --memory-limit=LIMIT
approximate total memory limit for all threads (by default 2GB)
--tmpdir=TMPDIR
directory for storing intermediate files; default is system directory for temporary files
-o, --out=OUTPUTFILE
output file name; if not provided, the result is written to a file with .sorted.bam extension
-n, --sort-by-name
sort by read name instead of coordinate (lexicographical order)
--sort-picard
sort by query name like in picard
-N, --natural-sort
sort by read name instead of coordinate (so-called 'natural' sort as in samtools)
-M, --match-mates
pull mates of the same alignment together when sorting by read name
-l, --compression-level=COMPRESSION_LEVEL
level of compression for sorted BAM, from 0 to 9
-u, --uncompressed-chunks
write sorted chunks as uncompressed BAM (default is writing with compression level 1), that might be faster in some cases but uses more disk space
-p, --show-progress
show progressbar in STDERR
-t, --nthreads=NTHREADS
use specified number of threads
-F, --filter=FILTER
keep only reads that satisfy FILTER

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Follow the checklist to report an issue Did you follow the https://github.com/biod/sambamba#check-list ?
Projects
None yet
Development

No branches or pull requests

2 participants