Cant find BAM input file or BAM index file #21
Description
when I run the step 2 of Retroseq, the software tell me: Cant find BAM input file or BAM index file
here is my whole command:
step 1: retroseq.pl -discover -bam MD1_INDEL_realigned.bam -output MD1_candidates.tab -eref eref.tab -align #no error message
step2: retroseq.pl -call -bam MD1_INDEL_realigned.bam -input MD1_candidates.tab -ref PK_ref.fa -output Retroswq_MD1.vcf
here is the error message:
RetroSeq: A tool for discovery of transposable elements from short read alignments
Version: 1.5
Author: Thomas Keane (thomas.keane@sanger.ac.uk)
Cant find BAM input file or BAM index file: MD1_INDEL_realigned.bam
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By the way, I'm using the samtools version: 0.1.19