Open hmyh1202 opened 6 years ago
my code: bedtools-2.25.0/bin/bedtools coverage -counts -sorted -a test.bed -b test.sort.bam
the bed was sorted using : sort -k1,1 -k2,2n the BAM file ( after PE reads ) was sorted by SAMtools using: sometools sort
some error was reported as below:
ERROR: chromomsome sort ordering for file test.sort.bam is inconsistentwith other files. Record was: chr1 10291 10504 D00612:288:HLTW7MCXY:9:2124:23195:38079 23 - ... ...
my code: bedtools-2.25.0/bin/bedtools coverage -counts -sorted -a test.bed -b test.sort.bam
the bed was sorted using : sort -k1,1 -k2,2n the BAM file ( after PE reads ) was sorted by SAMtools using: sometools sort
some error was reported as below:
ERROR: chromomsome sort ordering for file test.sort.bam is inconsistentwith other files. Record was: chr1 10291 10504 D00612:288:HLTW7MCXY:9:2124:23195:38079 23 - ... ...