BamCoverage

BamCoverage: A efficient software tools to Calculate site depth of genome based bam/sam List

The newest version of this funtion was integrated into toolkit BamDeal ,please replace BamCoverage by this BamDeal.

           ./BamDeal statistics  Coverage

1. Install

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Please replace BamCoverage with this toolkit BamDeal.

1. Install

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 This software rely htslib，so should Pre-install htslib first samtools-1.5/htslib-1.5
Then Just [make] or [sh make.sh ] to compile this software.
the final software can be found in the Dir [bin/BamCoverage]

For linux /Unix and macOS

        tar -zxvf  BamCoverage-XXX.tar.gz
        cd BamCoverage-XXX;                             # if Link do not work ,Try re-install  two  library
        cd src;                                         #【zlib and htslib】 and copy them to the library Dir
        make ; make clean                               # BamCoverage-XX/src/include/zlib 
        ../bin/BamCoverage                              

2. Example

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• 1. Calculate bam files

#To Calculate bam

    ./bin/BamCoverage  -List  bam.list  -OutPut  out.depth.fa.gz -MinQ -1
   # To out Put the each chr meanDepth Coverage add [-Stat]
    ./bin/BamCoverage  -List  bam.list  -OutPut  out.depth.fa.gz  -Stat

• 2. Calculate sam files

# To cCalculate sam
	./bin/BamCoverage  -List  sam.list  -OutPut  out.depth.fa.gz  -Stat
# Also you the  add the  -MinQ to filter some reads
	./bin/BamCoverage  -List  sam.list  -OutPut  out.depth.fa.gz  -MinQ 10

• 3. Calculate GC-Depth Dis Figure

# First Out Put the Depth-GC wig info with [-Ref  Ref.fa]
	./bin/BamCoverage  -List bam.list   -OutPut outFix   -Ref Ref.fa  -Stat
# Second To Plot the Figure 
# Must PreInstall R with library ggplot2,gridExtra,ggExtra
	perl  bin/GC_Depth_Plot.pl  outFix.DepthGC.wig.gz  MaxDepth  OutFig

3. Introduction

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• Parameter description

  ./BamDeal   statistics  Coverage

        Usage: Coverage  -List  <bam.list>  -OutPut  <outFix>

                -InList    <str>     Input Bam/Sam File List
                -InFile    <str>     Input Bam/Sam File File[repeat]
                -OutPut    <str>     OutPut File prefix

                -Ref       <str>     In Ref.fa If Want Out Depth-GC wig info
                -Windows   <int>     Windows size for Depth-GC wig[10000]
                -Bed       <str>     Stat Coverage,MeanDepth for these bed Regions
                -Stat                Stat Coverage,MeanDepth & Depth Dis of whole-genome

                -MinQ      <int>     Filter the read low mapQ[10]

                -help                Show this help [hewm2008 v1.30]

4. Results

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Format Introduction

• sam bam format

5）Discussing

• email: [email protected] / [email protected]
• join the QQ Group : 125293663

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