I am trying to convert my bam file into two fastq files in the command line, but I run into an error and I'm not sure what to change/do differently. Thoughts/advice?
bedtools bamtofastq ID18_Father_exome_L001_001_mtExtract.qsort.bam -fq test1.fq -fq2 test2.fq
*****ERROR: Unrecognized parameter: ID18_Father_exome_L001_001_mtExtract.qsort.bam ***** ***** *****ERROR: Need -bam. ***** Tool: bedtools bamtofastq (aka bamToFastq) Version: v2.17.0 Summary: Convert BAM alignments to FASTQ files. Usage: bamToFastq [OPTIONS] -i <BAM> -fq <FQ> Options: -fq2 FASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name is creating paired FASTQ. -tags Create FASTQ based on the mate info in the BAM R2 and Q2 tags. Tips: If you want to create a single, interleaved FASTQ file for paired-end data, you can just write both to /dev/stdout: bedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq
As I was writing the question, I realized that I didn't include the -i before the bam file name, however including it resulted in the following error:
error: unrecognized command: -i