bedtools报错：ERROR: Sort order was unspecified，Please rerun with the -g option for a genome file

运行命令bedtools coverage -sorted -a ${path1}/input/gencode.v19.annotation.bed -b $file > ${result}/${tissueName}.coverage.txt出现的报错。
解决方案：删除bed文件的chr即可。如下所示：

${path1}/input/gencode.v19.annotation.bed

${path1}/input/gencode.v19.annotation.nochr.bed：

重新运行即可：
bedtools coverage -sorted -a ${path1}/input/gencode.v19.annotation.nochr.bed -b $file > ${result}/${tissueName}.coverage.txt