Hi im doing Variant calling on fastq files for which i have 4000 fq files and the variant calling are done in different 9 steps. Each step generate different files that are output to next steps.
So can anybody help me with this to do it in a loop it pick up names from previous steps for all files. Step 1 command is here:
bwa mem -M -R '@RG\tID:ERR040140\tLB:2517707\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR040140' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR040140_* > ERR040140.sam
So i made an excel file to break the command in columns so that i can change the file names keeping remaining command same just like this:
So changes are occurring 5th, 7th and 9th column. which are:
tID:ERR040140 tLB:2517707 tSM:ERR040140 ERR040140_* ERR040140.sam
Can anyone help me with loop or something?