Calculating coverage - Revision history

Rf at 22:42, 4 March 2017

2017-03-04T22:42:53Z

Rf at 13:57, 30 June 2016

2016-06-30T13:57:30Z

Rf at 13:53, 30 June 2016

2016-06-30T13:53:05Z

Rf at 13:03, 30 June 2016

2016-06-30T13:03:15Z

Rf at 16:53, 28 June 2016

2016-06-28T16:53:25Z

Rf: Created page with "= Introduction = Coverage can be calculated in several different ways and this pages aims to describe a few of them = Bedtools genomecov = This is one of the most commonly..."

2016-06-28T16:48:23Z

Created page with "= Introduction = Coverage can be calculated in several different ways and this pages aims to describe a few of them = Bedtools genomecov = This is one of the most commonly..."

New page

= Introduction =

Coverage can be calculated in several different ways and this pages aims to describe a few of them

= Bedtools genomecov =

This is one of the most commonly used methods and requires loading of the bedtools module. The base of the command is
bedtools genomecov -bga -ibam <bamfile>

@@ Line 1: / Line 1: @@
 = Introduction =
-Coverage can be calculated in several different ways and this pages aims to describe a few of them
+Coverage can be calculated in several different ways and this pages aims to describe a few of them.
-= Bedtools genomecov =
+The most prominent of the coverage tools is probably the bedtools suite.
 This is one of the most commonly used methods and requires loading of the bedtools module, also used in the callSNPs.py tool. The base of the command is
@@ Line 10: / Line 12: @@
 <u>Explanation</u>:
 * the '''-bg''' option is for bedgraph
 == in a script with AWK ==
@@ Line 29: / Line 33: @@
           bedtools genomecov -bga -ibam $BF |awk -v t=$2 '{if($4>=t) {j=$3-$2;i=i+j;SUM=SUM+$4*j;}} END {print SUM/(i+0.0);}'
   done

@@ Line 27: / Line 27: @@
   for BF in ${ARRAY[@]}; do
           echo -n "$BF: "
-          bedtools genomecov -bga -ibam $BF |awk -v t=$2 '{if($4>=t) {j=$3-$2+1;i=i+j;SUM=SUM+$4*j;}} END {print SUM/(i+0.0);}'
+          bedtools genomecov -bga -ibam $BF |awk -v t=$2 '{if($4>=t) {j=$3-$2;i=i+j;SUM=SUM+$4*j;}} END {print SUM/(i+0.0);}'
   done

@@ Line 8: / Line 8: @@
   bedtools genomecov -bga -ibam <bamfile>
-<u>Explanation</u>
+<u>Explanation</u>:
 == in a script with AWK ==

← Older revision		Revision as of 13:03, 30 June 2016
Line 8:		Line 8:
	bedtools genomecov -bga -ibam <bamfile>		bedtools genomecov -bga -ibam <bamfile>

−	Explanation	+	<u>Explanation</u>
		+
		+	== in a script with AWK ==
		+
		+	Here is an example script for using '''genomecov''' with AWK to calculate coverage
		+
		+	#!/bin/bash
		+	EXPECTED_ARGS=2
		+	if [ $# -ne $EXPECTED_ARGS ]; then
		+	echo "This script uses awk to calculate average coverage in a bamfile. It needs $EXPECTED_ARGS arguments"
		+	echo "Correct usage: $0 <subfolder_with_all_the_bamfiles>> <minimum_coverage_value>"
		+	exit
		+	fi
		+	module load bedtools
		+	O=$(find $1 -iname "*.bam")
		+	ARRAY=( $O )
		+	for BF in ${ARRAY[@]}; do
		+	echo -n "$BF: "
		+	bedtools genomecov -bga -ibam $BF \|awk -v t=$2 '{if($4>=t) {j=$3-$2+1;i=i+j;SUM=SUM+$4*j;}} END {print SUM/(i+0.0);}'
		+	done