Hi.

I have one problem while running Dindel stage 1.

Command:

dindel --analysis getCIGARindels --bamFile mybamfile.bam --outputFile mybamfile.dindel_output --ref hg19.fasta

When working for indel stage 1, the monitor shows the error message;

error: faidx error, len==0

I used latest samtools(ver 1.2) for indexing the fasta file and bam file(.fai , .bai)

Also variants.txt file is made successfully. But libraries.txt file is empty.

I am wondering why the problem comes up.

Please let me know about this issue.