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Old 03-20-2016, 01:12 AM   #1
Alphabets
Junior Member
 
Location: SZ

Join Date: Mar 2016
Posts: 7
Default lobSTR dealing with the paired-end BAM file

Hello:

I use the software lobSTR to deal with the paired-end bam file. As the document shows, I should run the follow code before the bam file sorted by read name.

'''
lobSTR \
--index-prefix hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ \
-f my_sample.bam --bampair \
--rg-sample my_sample.sorted.bam --rg-lib my_sample \
--out my_sample_output
'''

My question is which bam file ir right in the above code's third line and fourth line, the bam before sorted or after sorted?
The document shows there should be the bam file before sorted, but I think it should be the sorted rather than the raw bam file in the third line.
Besides, I think the fourth line should be a tag not the sorted file.

Any other ideas about it and could anyone solve my confusion. Thanks!
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