bwa mem and pindel
Dear all,
Thank you very much to all of you in advance for all the help I am sure I will receive. I am having problems running Pindel on bam files generated by bwa mem -M option. Pindel is not able to find reads in any chromosome. In all of them I get:
Looking at chromosome Chr1 bases 0 to 10000000.
Insertsize in bamreads: 250
Number of reads in current window: 0, + 0 - 0
Number of reads where the close end could be mapped: 0, + 0 - 0
Percentage of reads which could be mapped: + 0.00% - 0.00%
and at the end all output files are empty. I double checked the refererence file to be sure that it was the same used for the alignment. I suspect that -M option in BWA MEM could be the cause. Any insight of why this could happen? I need to run BWA MEM with -M option in order to mark duplicates, any alternative?
Thanks again in advance.
Best Regards,
Nacho
Thank you very much to all of you in advance for all the help I am sure I will receive. I am having problems running Pindel on bam files generated by bwa mem -M option. Pindel is not able to find reads in any chromosome. In all of them I get:
Looking at chromosome Chr1 bases 0 to 10000000.
Insertsize in bamreads: 250
Number of reads in current window: 0, + 0 - 0
Number of reads where the close end could be mapped: 0, + 0 - 0
Percentage of reads which could be mapped: + 0.00% - 0.00%
and at the end all output files are empty. I double checked the refererence file to be sure that it was the same used for the alignment. I suspect that -M option in BWA MEM could be the cause. Any insight of why this could happen? I need to run BWA MEM with -M option in order to mark duplicates, any alternative?
Thanks again in advance.
Best Regards,
Nacho