Difference between revisions of "Usefull small commands scripts etc"
From mn/bio/cees-bioinf
(Created page with "<div> ==== Quick command to index a bunch of bam files ==== <div><u><span style="font-size: 12px;">Use case:</span></u></div></div> *you have a set of bam files, some (or all)...") |
|||
Line 1: | Line 1: | ||
<div> | <div> | ||
==== Quick command to index a bunch of bam files ==== | ==== Quick command to index a bunch of bam files ==== | ||
− | <div><u><span style="font-size: 12px;">Use case:</span></u | + | <div><u><span style="font-size: 12px;">Use case:</span></u></div> |
*you have a set of bam files, some (or all) of which are not yet indexed | *you have a set of bam files, some (or all) of which are not yet indexed | ||
*you want to run 'samtools index' on those that are not yet indexed | *you want to run 'samtools index' on those that are not yet indexed | ||
Line 7: | Line 7: | ||
<div><br/></div><div><u>Solution:</u> use the makefile I created for this: /projects/cees/scripts/makefiles/index_all_bams.mk</div><div><br/></div><div><u>Usage:</u></div><pre>cd path/to/folder/with/bam/files | <div><br/></div><div><u>Solution:</u> use the makefile I created for this: /projects/cees/scripts/makefiles/index_all_bams.mk</div><div><br/></div><div><u>Usage:</u></div><pre>cd path/to/folder/with/bam/files | ||
module load samtools | module load samtools | ||
− | make -f /projects/cees/scripts/makefiles/index_all_bams.mk</pre><div><span style="font-size: 12px;">To run this in parallel, add the '-j' flag and the number of threads to start:</span></div><pre>make -j 5 -f /projects/cees/scripts/makefiles/index_all_bams.mk</pre><div><u>Author:</u> Lex Nederbragt</div> | + | make -f /projects/cees/scripts/makefiles/index_all_bams.mk</pre><div><span style="font-size: 12px;">To run this in parallel, add the '-j' flag and the number of threads to start:</span></div><pre>make -j 5 -f /projects/cees/scripts/makefiles/index_all_bams.mk</pre><div><u>Output:</u></div> |
+ | *For each .bam file, a corresponding .bam.bai file | ||
+ | <div><u>Notes:</u><br/></div> | ||
+ | *if any .bam file present in the folder already has a corresponding .bam.bai file, his bam file will not be indexed | ||
+ | <div><u></u><br/></div><div><u>Author:</u> Lex Nederbragt</div> |
Latest revision as of 09:57, 9 December 2014
Quick command to index a bunch of bam files
Use case:
- you have a set of bam files, some (or all) of which are not yet indexed
- you want to run 'samtools index' on those that are not yet indexed
- (optional) you would like to run this in parallel
Solution: use the makefile I created for this: /projects/cees/scripts/makefiles/index_all_bams.mk
Usage:
cd path/to/folder/with/bam/files module load samtools make -f /projects/cees/scripts/makefiles/index_all_bams.mk
To run this in parallel, add the '-j' flag and the number of threads to start:
make -j 5 -f /projects/cees/scripts/makefiles/index_all_bams.mk
Output:
- For each .bam file, a corresponding .bam.bai file
Notes:
- if any .bam file present in the folder already has a corresponding .bam.bai file, his bam file will not be indexed
Author: Lex Nederbragt