Samtools Merge and rmdup

[AvinashP]

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

[nilshomer]

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

All answers can be found using the "site:seqanswers.com" in a google search. Post back if you don't find them!

[AvinashP]

Thanks,
but i faced difficulty finding the right answers.
Can you please point me to any links giving the answers ?

Thanks