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Top Forums Shell Programming and Scripting mapped reads using samtools flagstat options Post 302707043 by @man on Friday 28th of September 2012 06:27:54 AM
Old 09-28-2012
mapped reads using samtools flagstat options

Hey guys,

Does anyone know how to calculate total number of mapped reads for a certain region of a bam file using samtools flagstat?
I know to use flagstat for the whole bam file. but for a specific region of it... is there an option?

Tnx

---------- Post updated at 12:27 PM ---------- Previous update was at 05:50 AM ----------

Oh I just realized that the tool was "samtools view" which is able to calculate the mapped reads of a certain region of a given bam file.

But I don't know how to do it yet; and which options should I use.
 

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DBS-EDIT-PATCH(1)						Debian Build System						 DBS-EDIT-PATCH(1)

NAME
dbs-edit-patch - Edit a DBS patch SYNOPSIS
dbs-edit-patch [options] patch dbs-edit-patch -h|--help DESCRIPTION
dbs-edit-patch is script to generate or modify patches for Debian source-packages in DBS format. WARNING
dbs is deprecated, please switch to the `3.0 (quilt)' Debian source package format instead. See http://wiki.debian.org/Projects/Deb- Src3.0#FAQ for a short guide how to do it. OPTIONS
-h, --help Show summary of options. -t dir, --tmpdir=dir Directory for the temporary files, default is /tmp or if set $TMP. -s dir, --sourcedir=dir Top level directory of the debian-package source-tree, default is the present working directory. -P dir, --sourcepatchdir=dir Directory containing upstream patches. -T dir, --sourcetardir=dir Directory containing the upstream tarball. -p level, --strip=level Striplevel -p of patch (Option -p of diff(1)), accepted values are 0 and 1, default is 0. ENVIRONMENT VARIABLES
TMP Sets the directory for the temporary files, can be overridden with -t dir. debian/vars dbs-edit-patch will automatically use variables defined in the optional debian/vars file. When a file debian/vars.in exists and debian/vars either does not exist or is older than any of the following files: debian/vars.in, debian/changelog, debian/rules or debian/control, then dbs-edit-patch will try updating the vars file by running the following command make -f debian/rules -W debian/vars.in debian/vars EXAMPLES
Edit the 021_debian patch of Heimdal: ~/heimdal-0.3d> dbs-edit-patch -t/tmp 021_debian Extracting source heimdal-0.3d.tar.gz ... successful. Applying patch 001_replay ... successful. etc. Copying heimdal-0.3d to heimdal-0.3d-old ... successful. Applying patch 021_debian ... successful. Edit files under /tmp/021_debian/heimdal-0.3d as required, then put a short description into /tmp/021_debian/patch-description if desired, and finally execute /tmp/021_debian/dbs-update-patch to save the results. Technical note: dbs-edit-patch extracts all patches before 021_debian into /tmp/021_debian/heimdal-0.3d, copies the result to /tmp/021_debian/heimdal-0.3d-old, and applies the last patch 021_debian (if it exists). Also, it creates a shell script which will create the diff between the old and new directories: ~/heimdal-0.3d> ls -la /tmp/021_debian total 12 -rwxr-xr-x 1 bam users 112 Jan 31 13:31 dbs-update-patch* -rw-r--r-- 1 bam users 0 Jan 31 13:31 patch-description drwxr-xr-x 14 bam users 4096 Jan 31 13:31 heimdal-0.3d/ drwxr-xr-x 14 bam users 4096 Jan 31 13:31 heimdal-0.3d-old/ drwxr-xr-x 5 bam users 4096 Jan 31 13:31 .stampdir/ ~/heimdal-0.3d> cat /tmp/021_debian/dbs-update-patch #!/bin/sh -e cd "/tmp/021_debian" HOOK_DIR="/usr/src/heimdal/debian/dbs-hooks" test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-prediff find -name "*.bak" -print0 | xargs -0 --no-run-if-empty rm find -name "*~" -print0 | xargs -0 --no-run-if-empty rm : > new_patch test ! -e patch-description || cp patch-description new_patch diff -ruN heimdal-0.3d-old heimdal-0.3d >> new_patch || test $? -eq 1 mv new_patch /usr/src/heimdal/debian/patches/021_debian test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-postdiff SEE ALSO
diff(1), dbs(7), /usr/share/doc/dbs/ AUTHOR
DBS was written by Adam Heath, modified by Ben Collins, modified and packaged for Debian by Brian May. This manpage was generated by Andreas Metzler and modified by Robert Luberda. Debian February 15th, 2011 DBS-EDIT-PATCH(1)
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