We have 100 exomes in one folder on our server, all are stored as a fastq file. What I did until now, was creating index and get ready for the alignment with the following lines:
bwa index -a hg38.fa samtools faidx hg38.fa java -jar $PICARD CreateSequenceDictionary REFERENCE=hg38.fa OUTPUT=hg38.dict
Now, the alignment of each exome is the next step, though I am looking for a way to align align all 100 exoms in one command, I don't want to copy/paste the same thing a hundred times. Our exome files have a very generic name, named from 1 to 100.fq
Any clue how I can do that?