RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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
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 ############## By the way, I'm using the samtools version: 0.1.19