hi,
I have 7 bam files which i need to merge into a single one.
1. Should i first sort the bam files and then merge or merge it first and then sort ?
2. Is it important to do a 'rmpup' ? Does removing duplicates really helps in SNP calling ? or is it optional ?
3. What are the options -r and -h do ? Are they important if if i don't use a 'rmdup' after that ?
I have started using bwa with samtools.
Thanks
I have 7 bam files which i need to merge into a single one.
1. Should i first sort the bam files and then merge or merge it first and then sort ?
2. Is it important to do a 'rmpup' ? Does removing duplicates really helps in SNP calling ? or is it optional ?
3. What are the options -r and -h do ? Are they important if if i don't use a 'rmdup' after that ?
I have started using bwa with samtools.
Thanks
Comment