samtools和picard统计的话都会强制忽略dup标记的reads，统计结果与igv软件查看的bam文件不符

需求统计bam文件的各个位点真实碱基分布情况

使用软件： bam-readcount，统计bam文件得到真实的碱基分布

1 ：参考基因组序列，fasta格式即可 2 ：bwa比对的bam结果文件，比对使用的参考基因组需要保持一致

示例路径： /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/example

天津集群脚本以及流程：

/bin/rm  -rf  /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/example/95-04___9501full.txt
mkdir  -p   /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/example/95-04___9501full.txt
ln -sf   /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/3.pag/X101SC23065193-Z01-J009.20231009.pagpipline.zidingyi9batchs/ref_9501full/9501full.txt  /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/example/95-04___9501full.txt
genome=`ls /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/example/95-04___9501full.txt/*`
/PUBLIC/source/HW/Disease/bin/samtools   faidx    $genome
awk '{print $1, 1, $2}'   ${genome}.fai   | sed -e 's/ /\t/g'  >   ${genome}.fai.bed

python   /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/bam-readcount-statbam.py  --fa  $genome   --bam  /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/3.pag/X101SC23065193-Z01-J009.20231009.pagpipline.zidingyi9batchs/ref_9501full/Mapping/95-04/95-04.final.bam  --bed   ${genome}.fai.bed  --outfile  /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/example/95-04___9501full.txt/bam-readcount-stat.tmp

python   /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/stat_tmpfile.py   --infile   /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/example/95-04___9501full.txt/bam-readcount-stat.tmp   --outfile    /TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/jiftools/bam-readcount/example/95-04___9501full.txt/bam-readcount-stat.xls